When I try and edit the scripts I just get a big
;CODE NOT LOADED
Could it have something to do with the fact that we are using Version Control? I merge the changes my team makes to the mod into a master .esm file.
Or do I have to do that thing that people are doing with dawnguard? Where you have to add the .bsa file to some config list or something(i've heard)

I'd imagine when all the PEX files are present, all will load, but you might need to reload the plugin first.