I make all my tweaks in a different file that loads just before the merged patch.
Active Mod Files:00 fallout3.esm01 anchorage.esm02 thepitt.esm03 brokensteel.esm04 pointlookout.esm05 zeta.esm06 Unofficial Fallout 3 Patch.esm [Version 1.2.0]07 Destruction.esm08 PointLookout-FollowersGetToGo.esm [Version 2.]09 Impervious Power Armour.esm0A craft.esm0B calibr.esm [Version 1.4]0C xcalibr.esm0D Project Beauty.esm0E refurbishes [all].esm0F CubeExperimental (EN).esm10 Zumbs' Overhauled Real Time Security.esm11 FO3 Wanderers Edition - Main File.esm12 mart's mutant mod.esm13 Companion Core.esm14 Companion Share & Recruit.esm15 RobCo Certified v2.esm16 Wasteland Whisperer v2.esm17 Enhanced Weather - Rain and Snow.esm18 StreetLights.esm19 dcinteriors_comboedition.esm1A Unofficial Fallout 3 Patch - Operation Anchorage.esp [Version 1.2.0]1B Unofficial Fallout 3 Patch - The Pitt.esp [Version 1.2.0]1C Unofficial Fallout 3 Patch - Broken Steel.esp [Version 1.2.0]1D Unofficial Fallout 3 Patch - Point Lookout.esp [Version 1.2.0]1E Unofficial Fallout 3 Patch - Mothership Zeta.esp [Version 1.2.0]1F FireLightFix.esp20 DarNifiedUIF3.esp21 StreetLights - Wasteland.esp22 TinCanCRAFTing.esp [Version 2.0]23 CRAFT - EnergyAmmo.esp24 CALIBRxMerchant.esp25 InverseCombatKnife.esp26 More Hotkeys.esp27 Princess Better Prompts v1pt1.esp28 Zombie Sounds V2.esp29 GeneratorSound.esp2A Moshman's Wasteland Ambiance.esp2B GalaxyNewsRadio100[M].esp2C RadioBlues.esp2D WAR_radio.esp2E People_Radio.esp2F InvasionRadio.esp30 KBATRadio.esp31 VTAP25.esp32 GhostRadio.esp33 mutantradio.esp34 LookoutRadio.esp35 RadioTenpenny.esp36 Radio Stutter fix.esp37 RadioHotkey.esp38 RadioHotkey_RadioBluesAddon.esp39 CONELRAD 640-1240.esp3A Existence2.0.esp3B UPP - Pack 1.esp3C UPP - Pack 2.esp3D UPP - Original Perks.esp3E UPP - Experience Perks.esp3F UPP - Quest Perks.esp40 PreWar Book Titles and Perks.esp41 Combat Style Perks.esp42 NotSoFast.esp43 HeirApparent.esp44 BoSPatrols.esp45 MarkB50K_Wasteland_Patrols.esp46 tubRRCompound.esp47 Stealth Kills Enabled.esp48 Stealth Kills Enabled - Pitt Compatibility.esp49 Echo_BatteryCharger.esp4A HouseholdWaterPurifier.esp4B BlackWolf Backpack.esp4C GunnySack.esp [Version 1.3]4D 1Animated Nightvision goggles.esp4E Directional PipLight HDR.esp4F Expanded Megaton House V3.esp50 MaintenanceShed.esp [Version 1.3]51 merc.esp52 moremapmarkers.esp53 maxlevelworkaround-hp-bs.esp54 wastelandmastery.esp55 skillcheck.esp56 Treasure Maps_Underground.esp57 Treasure Maps_Secrets of the Wasteland.esp58 Treasure Maps_Bobblehead Edition.esp59 Treasure Maps_A Fist Full of Caps.esp5A Destruction - Main.esp5B Destruction - Main - Statics.esp5C Destruction - DLC.esp5D Destruction - DLC - Statics.esp5E MTC Wasteland Travellers.esp5F DCInteriors_DLC_Collectables.esp60 Rivet City Realignment.esp61 Greenerworld.esp62 MovinOnUp3.0.esp63 FO3 Wanderers Edition - Main File.esp64 FO3 Wanderers Edition - DLC Anchorage.esp65 FO3 Wanderers Edition - DLC The Pitt.esp66 FO3 Wanderers Edition - DLC Broken Steel.esp67 FO3 Wanderers Edition - DLC Point Lookout.esp68 FO3 Wanderers Edition - DLC Mothership Zeta.esp69 FO3 Wanderers Edition - Alternate Travel.esp6A FO3 Wanderers Edition - Optional Restore Tracers.esp6B FO3 Wanderers Edition - Optional VATS Realtime.esp6C FO3 Wanderers Edition - Project Beauty.esp6D FO3 Wanderers Edition - Project Beauty (Followers Enhanced).esp6E weaponmodkits.esp6F weaponmodkits - fwe master release.esp70 weaponmodkits - operationanchorage.esp71 weaponmodkits - thepitt.esp72 weaponmodkits - brokensteel.esp73 weaponmodkits - pointlookout.esp74 weaponmodkits - zeta.esp75 Echo_UseBothGloves.esp76 Tactical Weapons by gRs Frederyck.esp77 xcalibrmunitions.esp78 xcalibrmunitions_fosenhancements.esp79 ZL-ACR.esp7A ZL-SVD-CALIBR.esp7B Dogmeat Leather Armor - CRAFT.esp7C Dragonskin Tactical Outfit.esp7D DragonskinBonusPack.esp7E stealthboy recon armor - craft.esp7F calibr ammo schematics - craft.esp80 CRAFT Improvised Weaponry.esp81 CRAFT Improvised Weaponry - Unmodeled.esp82 Burnification.esp83 eve.esp84 eve operation anchorage.esp85 eve - fwe master release.esp86 EVE - FWE Master Release (Follower Enhanced).esp87 EVE Anchorage - FWE DLC Anchorage.esp88 EVE - FWE with WeaponModKits.esp89 FalloutFood.esp8A FalloutFoods - FWE Master Release.esp8B ZORTS - Custom HP - FWE.esp8C ZORTS - Disable FWE activate.esp8D Companion Core DLC Addon.esp8E Wasteland Whisperer v2 Broken Steel Addon.esp8F RobCo Certified v2 Mechanist's Edition.esp90 RobCo Certified v2 Zeta Addon.esp91 RobCo Certified v2 Omnipatch.esp92 Playing With Firepower.esp93 ThePitt-NoFireFollowers.esp94 Phalanx-Obedient-Dogmeat.esp95 DogmeatEssentialModv1.2.esp96 Move-Dogmeat.esp97 DogmeatStealth.esp98 ImmersiveHealth.esp99 mart's mutant mod.esp9A mart's mutant mod - dlc anchorage.esp9B mart's mutant mod - dlc the pitt.esp9C mart's mutant mod - dlc broken steel.esp9D Mart's Mutant Mod - DLC Point Lookout.esp9E mart's mutant mod - dlc zeta.esp9F Mart's Mutant Mod - FWE Master Release.espA0 Mart's Mutant Mod - Project Beauty + FWE.espA1 Mysteriouswoman_corsetntrousers.espA2 T3T_MiscItemIcons.espA3 ACRForFWE.espA4 SVDForFWE.espA5 DTOForFWE.espA6 Gifts4Kids.espA7 Realistic Death Physics.espA8 megalight.espA9 Enhanced Weather - Rainbows.espAA Enhanced Weather - Weather Sounds in Interiors.espAB Realistic Interior Lighting.espAC Realistic Interior Lighting - BS.espAD Realistic Interior Lighting - OA.espAE PiPBoy Light Range x4.espAF PiPBoy Yellow Light.espB0 xCALIBR_override_FWE5.espB1 FWE(v.5.04)+WMK_weapons_xCALIBRified.espB2 frederyck+FWE+xCALIBR.espB3 tubunarFWE.espB4 Merged Patch 1.esp