You can put all your Mods in one folder outside of your BZ2 install so that you can access the mods from different installs and then point to them using your custom startup .cfg, like so.
Doing so makes it a lot easier to access Mods with different versions and it saves space.
// Configure game file system
ConfigureFileSystem()
{
// Setup base data
ConfigureStream("base")
{
// Look in "! RD_Config" first
AddDirRecurse("I:\!BZ2_Mods\! RD_Config");
// Look in "Uler" first
AddDirRecurse("I:\!BZ2_Mods\uler");
// Look at Uler13 pak next
AddPack("I:\!BZ2_Mods\uler13.pak");
// Look in "maps13" next
AddDirRecurse("@rootdir\maps13");
// Look at pakfiles next
AddPack("@rootdir\patch13.pak");
AddPack("@rootdir\data.pak");
// Look in "data" last, and only last.
AddDirRecurse("@rootdir\data");
}
// Make it active
SetActiveStream("base");
// Optional, for mods -- the ability to put pilots & savegames in
// other directories. Commented out to simply demonstrate how to
// do it.
// SetPilotsDirectory("Ulerpilots");
// SetSavesDirectory("Ulersaved");
}