If you have a lot of repetitive stuff to setup, I suggest looking into creating macros and/or presets for it.
Or write a script, if you're into that at all.
Personally - and I apologize if this is not helpful to you - I'm not a fan of putting lots of layers/passes in single files. Means you either have to rerender everything to change one pass, or things get messy. That's not to say there's no room for improvement in dealing with them in Fusion...