Here is an edited private message I sent to a fellow forum user posted for others to see (even though normally I'm pretty much a stickler for using he official threads for everything).
Well first this is where I learned about merging:
http://www.gamesas.com/index.php?/topic/898653-a-guide-to-merging-with-tesivgecko/
http://www.gamesas.com/?showtopic=1068317
As well as asking a lot of questions of my gurus on this Vorians and Arthmoor.
Basically the idea is to not merge mods that conflict with each other or that need to be separate. You can run conflict filter in TES4edit to see if two (or more) mods conflict - if you see no red then you should be OK. If two mods affect the same cell (internal or worldspace) then it won't work. There may be also issues with mods that have the same scripts but Gecko does offer at least some options with that.
Arthmoor warns a lot about not merging landscape mods (as tempting and as many as they are) due to things at times being permanently stored in the save game file. I'd urge any reading this to read a few UL threads and see how often the request to merge them comes up and their very valid reasons not to.
Other concerns are that mods which are the masters of other mods usually need to be left as they are for them to continue working as masters. Then also be mindful of mods that are updated often as that would mean remerging often. I tend to focus on single purpose mods that are not updated often and touch very little of the worldspace and cells. Think about how annoying it would be to merge houses, move into one with all your stuff, then find a fatal error. Or quest mods where you get done with most of a mod to find a fatal error that occured from merging. The goal is to either merge mods that leave no legacy anyway or mods that you won't update often if at all.
Yes you can merge mods with ini - just make sure to package them too in the final result.
So that leaves mods that don't conflict, mods that are not often updated, and mods that are simpler in their nature. Script run mods some of the best I've found.
I've known others who merge all mods to be merged into one giant mod. I prefer not to merge all into one esp as it makes it harder to track down errors. On the other hand Petrus is way more thorough taking weeks to months to set up a game before he plays, so he knows what he is doing. I like to dive in more so I need to keep the errors to a minimum so I take the theme mods approach and merge mods with the same theme together. Ready? Here goes - these are the current success stories with merging:
UI Mods Merged:
Spoiler Easy Menus v1.03Toglable Quantity Prompt 3.2.0Vacuity 0.2DropLastPickedUpItem 1.1Scroll Yes or No 1Press Delete to PCB
Home Care Mods Merged:
Spoiler Decorator AssistantDecorator Assistant UnlockAuto Book PlacerReznods MannequinsUniversal Armor Stands
Game Tweaks Merged:
Spoiler Dousing the Flames 1.10Exterior Actors Have Torches 1.3 DTDungeon Actors Have Torches 1.6 DTWearable GS and DS armorSyc_AtHomeAlchemy_No_Bounty_v2SetsunaDummyTrainingSkycaptainsBloodTimekuerteeNoLootingDuringCombat
Stealth Mods Merged:
Spoiler M.O.E. Realistic Law Enforcement 1&2Mind Control Crime v1CLS-SneakyFeet 0.9.5sycHearNoEvil v1LockBash Omega v1.5
I Probably will be doing a magic tweaks, alchemy tweaks, and combat tweaks merger soon too. I've done them in the past but not satisfied.
Dialogues and Messages Merged:
Spoiler 1. Role Playing Dialogues V0.732. Lore Dialogues 300 v2.33. Oblivifall - Let's talk v1.14. Oblivifall - Something's Not Right v1.05. Really Immersive Messages v1.56. Think to Yourself v17. Cliff County Names 1.18. Cliff Better letters v1.29. Reneer Notes Mod 0.9210. Stop Dark Brotherhood v1.1011. Expanded Greetings v112. Talk with your hands v213. AKF Prayer Idles
Environment mods Merged:
Spoiler Natural Habitat by Max TealDistant Chapel BellsRainbowsFalling StarsRegrowing NirnrootsLouder Nirnroots
Now this next set is more difficult to master and some editing was required (but I forgot what on some of them).
Dungeon Mods Merged:
Spoiler 1. Gelden Halls2. Darbenshire Keep3. Fort Krakatus4. Ruins of Tarnesia5. Ruins of Nalcarum6. Cave of Lost Souls7. The Forgotten Tomb8. Pale Goblin Dungeon9. Old School Dungeons10. Lost Glory11. The Liches Lair12. The Forgotten Tower13. Asharnkibibi14. Zergoniplimat
SI Dungeon Mods Merged:
Spoiler Temple of ZealotsRuins of BrenfaCraze MazeDeepgraveLaughing Maw
Tamriel Houses Merged:
Spoiler Abandoned Mtn ShackAlchemsit Cove COBLAll things AlchemicalCastle KnightstoneDank Dark CaveFalls View Forgotten ChapelLinawiln HomeLireals RetreatMisty HideoutSilent Stones CampWaters edge CottageYellow Rose CottageWhite Tower
SI Houses Merged:
Spoiler Abandoned Mania CampBroken Promesis SwampCutter EstateInquisitors LodgeJagnot_Split HomesJagnot_SummitPointHouseMadness HideoutNew Sheoth HomesPond Cottage
With dungeons and houses you've got to make sure that they don't conflict with other mods as well because if anything goes wrong then you are going to have to remove it - and that can mean loss of quests, moving out of a house (I hate moving). The Tamriel Houses mod really is a bit over the top and I had to keep a list of mods it does conflict with - so I recommend only a few. What I look for in houses is Not free, Not bought, but earned.
That is more intermediate stuff. Advanced is actually modding altogether.
Other options to consider.
Merging an esp to its parent esp/esmMerging esp to esm is possible but tricky. No don't merge to Oblivion.esm. Using Gecko convert the parent to an esm (if it isn't already), then merge to master, The resulting plugin will be an esm so convert back to esp if that is what they both were to start with.
Mod CleaningAlso a good idea to clean mods before merging and check again after merging.
Setting Merge Priority Priority means what mod do you want to have priority if they both touch the same thing. Them touching the same thing may be bad for landcapes and cells but not so much game settings. If they do not conflict at all then it is fine to set all to 1.
Load OrderI merge them by theme. So the dungeon mods or house mods will go in that section, Game tweaks loading later, UI and Home care mods earlier. Just look at where the merged mods are in the load order then guesstimate.
Bash TagsLikewise look at what BOSS says for the individual mods and be wary that adding tags will mean the same for all mods tagged. A few instances I just live without the tag but mostly I avoid merging mods that require a lot of tagging.
PackagingI'd suggest packing all the resources for the new mod together - including meshes, textures, and mutliple ini if needed. This will eliminate the need for long term watching of what mod resources are installed and in what order. I
do not recommend OBMM for this level of complex resource watching. BAIN is best.
That should kick this off to a good start.
Though Pseron is right hand merging is more thorough - if you have the know how.