Personally I keep all the "extra" files in the Library folder and all the tables in the Tables folder. If you leave them zipped they will not function when loaded directly by FP. You would also possibly run into problems with zip files containing multiple builds and subfolders etc (unless you are re-zipping them and organizing them yourself).
For folder structures between different frontends you could always use the good old "subst" command to create new virtual paths. I'm sure there are a ton of windows type redirect apps out there too
