Some of the files like character select screens and such are packed with all the characters, so different mods would need to overwrite the same files, which the mod manager doesn't like. To stack mods with these conflicts, you either have to:
Remove any conflicting files between the mods
Build a custom pack for those files
I don't know anything about creating the mods, but I can assure you option 1 works fine for in-game graphics and voices.