Alright, I have FWE and MMM RC-5 and the FOIP compatibility patch installed. Everything seems to run fine in the game so far. However, when I run FO3Edit, it shows a few red conflicts. A lot of creature conflicts in the FOIP patch have to do with actor effects. As an example, crFeralGlowingOne has some ActorEffects like PerkIronFist1, BobbleUnarmed, PerkMS03DreamCrusher and PerkFinesse are in red. I tried summoning one of these creatures with the console and I didn't see anything out of the ordinary with him. There's also some faction problems with MMM and FOIP. FWE restore tracers mod has some conflicts with the speed of ammo. Maybe this stuff is normal and benign, but it'd be nice to know so I don't have problems later. I also want to throw more mods into the mix and would like to know what things I can ignore and what things should raise red flags. Other mods I'd like to add are Fellout, project beauty, EVE, wmk, FOOK2 and certain components of XFO like the xp tables.
Conflicts are rarely bad and in the case of the FOIP patch they are very deliberate. A conflict simply means that the last loaded mod wins the conflict and it's settings are used.
For example if a mod were to modify the damage of a weapon, it would of course conflict with the Fallout3.esm since it has different values. And if you have three mods modifying the same gun, the last one loaded wins.
Just because something is a bright red, doesnt mean something bad. Read the ReadMe before making any assumptions about what means what.