Yes, make the merged patch with all your mods activated, and remake it whenever you add something. Consider including Weapon Mod Kits as well- it's very useful in a FWE/MMM game, and is a FWE recommended addition.
FYI, here's what I did last time I installed FO3 + all DLC (GOTY, which is fully patched):
Installed UOP and DARNified UI then played through Vault 101 till the end before adding anything else.
Installed FWE and MMM + FOIPs (made a new merged patch for each step onward) and poked around a bit outside the vault.
Added
EVE, WMK and their FOIPs, ditto..
Added other stuff and decided what FWE options I wanted, ditto..
Finally, I ended up starting a new character and going through 101 again. It's worked out well... I'm almost lvl 23 and about to commence the second stage of the main quest.
As always, refer to the readmes. One thing many seem to miss is that most of the MMM optional esp's no longer need to be included...
Here's my load order (the game is not
perfectly crash free, but is very stable...)
Spoiler Fallout3.esm
Anchorage.esm
ThePitt.esm
StreetLights.esm
BrokenSteel.esm
PointLookout.esm
Zeta.esm
Unofficial Fallout 3 Patch.esm
CRAFT.esm
CALIBR.esm
EVE.esm
FO3 Wanderers Edition - Main File.esm
Mart's Mutant Mod.esm
Unofficial Fallout 3 Patch - Operation Anchorage.esp
Unofficial Fallout 3 Patch - The Pitt.esp
Unofficial Fallout 3 Patch - Broken Steel.esp
Unofficial Fallout 3 Patch - Point Lookout.esp
Unofficial Fallout 3 Patch - Mothership Zeta.esp
DarNifiedUIF3.esp
DN_RecyclingMachine.esp
Echo_BatteryCharger.esp
Sack of Holding.esp
1Animated Nightvision goggles.esp
MrSlackPants-NightVisionGogglesNoModel.esp
solarcharger.esp
MoreMapMarkers.esp
Treasure Maps_Underground.esp
Treasure Maps_Secrets of the Wasteland.esp
Treasure Maps_A Fist Full of Caps.esp
FO3 Wanderers Edition - Main File.esp
FO3 Wanderers Edition - DLC Anchorage.esp
FO3 Wanderers Edition - DLC The Pitt.esp
FO3 Wanderers Edition - DLC Broken Steel.esp
FO3 Wanderers Edition - DLC Point Lookout.esp
FO3 Wanderers Edition - DLC Mothership Zeta.esp
FO3 Wanderers Edition - Followers Enhanced (BrokenSteel).esp
FO3 Wanderers Edition - Optional Restore Tracers.esp
WeaponModKits.esp
WeaponModKits - FWE Master Release.esp
WeaponModKits - OperationAnchorage.esp
WeaponModKits - ThePitt.esp
WeaponModKits - BrokenSteel.esp
WeaponModKits - PointLookout.esp
WeaponModKits - Zeta.esp
RealFragGrenade3.esp
EVE.esp
EVE Operation Anchorage.esp
EVE - FWE Master Release.esp
EVE - FWE Master Release (Follower Enhanced).esp
EVE Anchorage - FWE DLC Anchorage.esp
EVE - FWE with WeaponModKits.esp
Mart's Mutant Mod.esp
Mart's Mutant Mod - DLC Anchorage.esp
Mart's Mutant Mod - DLC The Pitt.esp
Mart's Mutant Mod - DLC Broken Steel.esp
Mart's Mutant Mod - DLC Point Lookout.esp
Mart's Mutant Mod - DLC Zeta.esp
Mart's Mutant Mod - Master Menu Module.esp
Mart's Mutant Mod - FWE Master Release.esp
Mart's Mutant Mod - FWE Master Release + DLCs.esp
LED pipboy light extended.esp
Faster PipBoy Light.esp
merged.esp
Total active plugins: 63
Total plugins: 65