Modding a running game is fun actually. For when you need to change over for the PBM save, just move the modded files out of your data folder and move em back in when you're done.
Easiest way to remember is if you got a file that can only be used for one campaign but will crash the game if you try to load another save. descr_sm_resources is one such file (the 1.2 one anyway)