Reading through the guides I'm fairly confident I will be able to change downloaded mods into BAIN installers (so for that, THANK YOU!
). Only thing I'm unsure about are mods that aren't already archived. For example, I have downloaded a file designed to be merged in wyre bash which is a .scr file. I understand how the file works.. replacing/adding details over the other mod, but where do I place it? Does it go straight into the bash patches folder seperately? Or can I place it in an archive and under installers?
Also what do I do about installer, such as frans .exe for example? Do they HAVE to be installed
Lastly, I am also confused on install order. It states in the guide that install order is very important or just as important than the BOSS order. Because I've used BOSS for so long I've gotten lazy with ordering and have completely forgotten what order is best to install mods in. I noticed, as your guide displays, that wyre bash recommends using markers, are these groups within the markers meant to represent teh order in which you should install the mods? Or are they simply there to just keep them more organised?
If so, is it possible to let me know what order mods are installed best in? I have already read up on the FCOM mod install, should I just install FCOM after base install (after dlc/shivering isles) as described and then all other mods straight afterwards? Does it matter what order they are installed in after FCOM?
Nm, I should probably use this shouldn't I? http://tesivpositive.animolious.com/?page=guides_mod_installation&subpage=complete_installation_guide&step=7&method=b

Also what do I do about installer, such as frans .exe for example? Do they HAVE to be installed
Lastly, I am also confused on install order. It states in the guide that install order is very important or just as important than the BOSS order. Because I've used BOSS for so long I've gotten lazy with ordering and have completely forgotten what order is best to install mods in. I noticed, as your guide displays, that wyre bash recommends using markers, are these groups within the markers meant to represent teh order in which you should install the mods? Or are they simply there to just keep them more organised?
Nm, I should probably use this shouldn't I? http://tesivpositive.animolious.com/?page=guides_mod_installation&subpage=complete_installation_guide&step=7&method=b
Screen 13 of the Installers Advanced guide gives all the file and folder types currently recognised by Wrye Bash - .scr file? hmm, screensaver file?, I dont think that is related to an oblivion install. ( Think along the lines of personalizing your desktop, right click, screensavers usually end with .scr file extension, where you got the idea to merge one of those into a bashed patch I have no idea

.exe's are executeable files, usually an installer itself which will not be recognised in a Wrye Bash BAIN, its purpose I would imagine is to be run on its own (similar to the new Wrye Bash 291 Installer.exe)
And for Markers, purely for your own organisational purpose - But the recommended list is just a suggestion of marker names to give you an idea of where to place them ( and also based on users previous recommendations as to what categories of mods should overwrite others )....
? DLC - Create this marker Lowest in your install order (By default lowest is visually at the top, Highest at the bottom (Check the Order Column, High number = Highest))
------- If you have Official DLC's in BAINs put them here in your install order, Horsearmour, Orrery, VileLair, Mehrunesrazor, Spelltomes....
If you dont have any DLC's in BAINs (say you installed them off a GOTY DVD for instance) - No need for a DLC Marker
? Unofficial Patches
------- UOP, USIP, UOMP, UOP Supplementals here (And read the documentation as to which should overwrite the other - Arthmoors supplementals should overwrite both UOP and UOMP for instance, which also patch DLC's fixing bugs in the original Official versions above - hence why this category of installers should be higher than DLCs in the install order)
? DarN
? Sounds
? World textures - expandable
~snip~
Its just a good recommendation for an Install order for all different kinds of mods - and not to be confused with Load order under the mods tab.
How detailed you want to go into organising your BAINs is up to you, and further refining your install order is down to use of the Conflicts reports for each Installer.
Here's my current Install Order to compare how I use markers, I have my own names for markers and groups but I am confident what I want in game, is, and I used the general recommendation as a basis tailored to the content I have and the way I like to categorise them, some you will notice are later than the recommendation, DarN for instance does not conflict with anything else for me (well, apart from Display Stats but thats in the same category of mods and overwritten as necessary), so really can be anywhere in my install order, and UOP Supplementals I have installing after RAEVWD and AWLS because when I created this Arthmoors advice was his files which conflict with those mods were newer (that advice may be old already after developments I briefly read about earlier which happened this weekend just gone, and the fact I have a newer version of AWLS today too, which now should overwrite RAEVWD whereas the reverse used to be true) ...
Also note - Quite a few of the following are not fully installed, particularly in the body mod section where I have sub-packages you cannot see here where I am mixing up combinations of parts to achieve what I want in game - Just warning anyone reading this really if they think they can just grab the same file ID's and install them in this order they will have a fair few problems

Spoiler
Bain Packages:++ 000 - 1.Official GOTY SI KotN DLCs.7z (60B8D9AA) (Installed)++ 001 - 2.Official GOTY - BSAs.7z (7713F65A) (Installed)++ 002 - 3.Optimised_Distant_Land_MAX_1_1-15278.7z (F720203B) (Installed)003 - ==--UOPs--==++ 004 - 4.Unofficial_Oblivion_Patch_v3_2_0_Manual_BAIN-5296.7z (BCBA7B56) (Installed)++ 005 - 5.Unofficial_Official_Mods_Patch_v15_BAIN-9969.7z (59895567) (Installed)++ 006 - 6.Unofficial SI patch v1_4_0_BAIN-10739.7z (79CE866D) (Installed)007 - ==--Sounds--==++ 008 - 7.Louder_Nirnroots-5277.rar (1C92F999) (Installed)++ 009 - 8.AS_Rain_and_Thunder_Sounds_V1.7z (DF3DBAB0) (Installed)++ 010 - 9.Ambiant_Sound_FX_1-2-29676.rar (93165CB5) (Installed)011 - ==--Land-LOD-Weather--==++ 012 - 1.Bomrets_Detailed_Normal_Maps_for_Vanilla_Version_1_1-18430.rar (19757949) (Installed)++ 013 - 2.Brumbeks_Sky_Pack_1-1-14346-1.7z (B4AFAE81) (Installed)++ 014 - 3.RAEVWD-v1.9-20053.7z (4DFF0231) (Installed)++ 015 - 4.RAEVWD_SI_Edition-v1.6.1-20053.7z (71ECCC10) (Installed)++ 016 - 5.RAEVWD_Darker_Regal_IC_Texture_Pack-20053.7z (911475E6) (Installed)++ 017 - 6.RAEVWD_SI_Bomret_Textures-20053.7z (ABBE189F) (Installed)++ 018 - 7.Animated_Window_Lighting_System_-_Meshes_v5-4-0-19628-1.7z (7024D10F) (Installed)++ 019 - 8.AWLS_-_Brumbek_Mixed_Textures_v5-4-0-19628-1.7z (40381101) (Installed)++ 020 - 9.Better_Imperial_City_Textures-35907-1-0.7z (9660DE95) (Installed)++ 021 - 10.Unofficial_Patch_Supplementals-v3.3.3-27710.7z (B22A6E3A) (Installed)++ 022 - Unofficial Oblivion Patch - missing land fix.7z (D9CC6241) (Installed)++ 023 - 11.Phinix_Waterfix_v2-6680.zip (66703519) (Installed)++ 024 - 12.RedBag_-_Fog-33424.rar (694FDFF4) (Installed)++ 025 - 13.ImprovedSignsComplete-9498.rar (7B1F6919) (Installed)++ 026 - 14.Real_Wood_Road_Signs_Full-25429.rar (9FF09A61) (Installed)++ 027 - 15.Unique_Signs-25314.zip (FC0A6D23) (Installed)++ 028 - 16.Diverse Grasses 0.6 - Main.7z (082DA354) (Installed)++ 029 - 17.LowTriPolyGrass-33403.7z (C5ADC3C6) (Installed)++ 030 - 18.LowPolyTrees-33414.7z (9AA85BC1) (Installed)031 - ==--House-Dungeons-Castles-Quests--==++ 032 - Better_Dark_Brotherhood_Sanctuary-BAIN-22135-3-02.7z (75DEE90A) (Installed)++ 033 - Better_Abandoned_House_v1-22-BAIN-25319.7z (166C4B5C) (Installed)++ 034 - Better_Benirus_Manor_v4-7-BAIN-18054.7z (034F8828) (Installed)++ 035 - Better_Benirus_Manor_-_Helping_Hands-23146-2-0.7z (D64883A4) (Installed)++ 036 - A_Brotherhood_Renewed-31773.7z (A848C6B3) (Installed)++ 037 - Aleswell_Cottage_ver_2-28702-1.7z (8C378AD3) (Installed)++ 038 - Faregyl_Village-21562.rar (F182678F) (Installed)++ 039 - The_Ayleid_Steps_3_4-16316.7z (AFBC1590) (Installed)++ 040 - Vergayun-26643.7z (B5075A2F) (Installed)++ 041 - Feldscar-30000.7z (6982601D) (Installed)++ 042 - Shadowcrest_Vineyard_COBL-22810.7z (C24B9C58) (Installed)++ 043 - TIE-v1.43-35265.7z (17A39748) (Installed)++ 044 - Peruggias Passage v1.0.7z (B126FE5F) (Installed)++ 045 - Darkness Hollows1.6.7z (721CCD19) (Installed)++ 046 - PTArtifactsProperV11-29931.7z (911DD4EF) (Installed)++ 047 - ChapelShop.7z (51620888) (Installed)048 - ==--Body-Race--==++ 049 - 1.Cobl_172-21104.7z (BFECAEE3) (Installed)++ 050 - 2.Cosmetic Compilation Revived - Capucine-17042.7z (00C83C68) (Installed)++ 051 - 3.Exnem Female EyeCandy - (nvde) v1.0-10171.7z (49278D7E) (Installed)++ 052 - 4.HGECBody_v1dot21-BAIN.7z (C530A9C0) (Installed)++ 053 - 5.RobertMale_v5_plus_Average_BAIN-25365.rar (19FA4533) (Installed)++ 054 - 6.EVE_HGEC_BodyStock_and_Clothing_Wrye_Bash_BAIN_-24078.7z (26F960C6) (Installed)++ 055 - 7.OFF_1_1_7ZIP-35487.7z (FB9504E5) (Installed)++ 056 - 8.CW_SOO-Vanilla-Heads-36387-1.7z (BB3DF284) (Installed)++ 057 - 9.Luchaires_Khajiit_Fix-31156.7z (F067285F) (Installed)++ 058 - 10.Foxs_Female_Argonian_textures_for_Exnems_body_v11-10506.rar (C068570D) (Installed)++ 059 - 11.DesuChan_Kawa_BodyTextures-For-Khajiit_RM-HGEC-Ver_2_0_1-35579.7z (8F39DF88) (Installed)++ 060 - 12.Exlorians_Khajiit_Tail_for_HGEC-33745.rar (5E9DD6F1) (Installed)++ 061 - 13.The_n_Dywyll_Elves-35397.7z (AB7F2FE4) (Installed)++ 062 - 14.SP_Hair_Pack_Beta_Ver_1_0-30707.7z (4640AFFD) (Installed)063 - ==--Companion-Creatures--==++ 064 - Companion_Vilja_ver_3-28977.7z (7FACA9AA) (Installed)++ 065 - Xtudos_Noise_Rerduction_for_Vilja_ver_3_bsa-28977.rar (29BFEF29) (Installed)++ 066 - Companion_Vilja_3_0_1_patch-28977.7z (F7BBCB3B) (Installed)++ 067 - Vilja_Customization_pack_3_0_1-With-Alt-Xtudo-28977.7z (4D9E24FF) (Installed)++ 068 - Vilja_in_Aleswell-28977-1.7z (3AE7AC78) (Installed)++ 069 - Cool_Hair_for_Vilja-28977.7z (F89A9287) (Installed)++ 070 - TIE Cats Full v1.0-34872.7z (07AB2D2E) (Installed)++ 071 - slofs_horses_base_2-24312.7z (3EFC924F) (Installed)++ 072 - Espless_Slofs_Horse_Replacer-27675.7z (39EF0C00) (Installed)++ 073 - Little_Baron_Vermin_1p5-35913-1p5.7z (A31D2C4A) (Installed)++ 074 - Little_Baron_Water_Beasts_v_1p3-36111-1p3.7z (B86F8943) (Installed)++ 075 - Deadlier_Creatures_V2-31882.rar (09BC037C) (Installed)076 - ==--Armour-Clothing-HGEC--==++ 077 - Sister_Of_Eisen-HGEC-25389.7z (A44B41F3) (Installed)++ 078 - Dark_Sisterhood_armor-28583.7z (6B13A5CC) (Installed)++ 079 - Underworld_armor-25734.rar (C5D41A92) (Installed)++ 080 - ExnemEC_Warrior01-13208.7z (AC25743C) (Installed)++ 081 - BaronArmorFull_fix-35464.7z (562F83E6) (Installed)++ 082 - Eyen Vampire hunter-Luchaire-1_2-19822.7z (8CED423C) (Installed)++ 083 - Gizmodian_-_Shell_of_the_Artifice-32969.7z (A6C9DF0E) (Installed)++ 084 - EY_Queensarmory-19531.7z (FA9E7AAE) (Installed)++ 085 - Captain_Molly_HGEC-28765.7z (BC382B0E) (Installed)++ 086 - Westwind_Rogue_HGEC-27319.7z (15755255) (Installed)++ 087 - IndigoArmor_v1_1_1_Fix-16645.7z (4F382ECC) (Installed)++ 088 - Elwing_Outfits_for_HGEC_v1_1-22330.7z (0C9700D0) (Installed)++ 089 - Rose_Corsets_-_Dark_and_Light_Combined-32429.7z (DB96C76F) (Installed)++ 090 - Minibloomers_v1_1-BAIN-36177-1-1.7z (AFE898DF) (Installed)++ 091 - Neck Seam Concealer Version_1_2-18669.rar (E942D40B) (Installed)092 - ==--Weapons--==++ 093 - SothaDagger_-_The_Ornate_Dwemer_Blade-24236.rar (A9231713) (Installed)++ 094 - Nicos_Tabaxi_Bows_v1_0-17444.rar (41579318) (Installed)++ 095 - Blade of Woe and Sufferthorn Replacer.rar (92842CB0) (Installed)++ 096 - Pekka_Shields_v12-14821.7z (7B4ACE88) (Installed)++ 097 - Explosives_v1_2-32267-1-2.7z (30D87C38) (Installed)098 - ==--Misc-Placers--==++ 099 - VAs_Better_Gold_with_No_Menu_Icon-5122.rar (DDF03442) (Installed)++ 100 - Improved Soulgems for TIE.7z (C70A668A) (Installed)++ 101 - Better_Potion_Bottles_Reduced_1dot2-14347.7z (93FC23BE) (Installed)++ 102 - better.looking.toolsv1.2.7z (13B10721) (Installed)103 - ====Game UI - Mechanics====++ 104 - DarkUId_DarN_16_Manual_Version-BAIN-11280.7z (04E2711F) (Installed)++ 105 - Display_Stats_1_3_1-31855-1-3-1.rar (43364AA0) (Installed)++ 106 - Metallicow_Cursor_Mod_v1-35856-1.7z (883CCACD) (Installed)++ 107 - Cyrodiil_Terrain_Map_v25-2634.7z (10CA4276) (Installed)++ 108 - Streamline_31_BAIN-22170.7z (EF2FECEC) (Installed)++ 109 - Wrye Bash INI Tweaks Xtras.7z (44070A39) (Installed)110 - ==Last==-- 111 - Vilja_ver_3_Documentation-28977.7z (F549731B) (Not Installed)
As you may have guessed I dont use FCOM, MMM, OOO (prefer T.I.E personally for a more stable game on less than cutting edge machines, and its easier to manage for the family setup here), so what you do with frans.exe I would suggest you read the install instructions, and as you guessed, TomLongs marvellously detailed expansion on those subjects
EDIT: And please note - I do not want this topic to diverge into a solve your personal installation problems dialogue, the discussion here is development of the Wrye Bash Pictorial Guides - If you need further help open a new topic.