What in the world? Sounds like you have something messed up o_o
Most mods, if not all of them, are "modfoldered". You should see different folders for mods in your mods folder, in the MEdieval 2: Total War folder within the SEGA folder in My Programs
For example, you would see IB2 Britanniae as the folder, or something to that effect
Anyway, installation for this mod is simple enough. If you already have IB2 Britanniae, download the two parts in the Download thread on this forum, that are titled IB2 Convestes Britanniae II. Then put the contents of the one titled mods into your IB2 Britanniae folder, replace all files. Take the second part, titled data, and put it into the IB2 Britanniae folder, replace all files it asks to replace
Should be good to go