I keep all my islands in a mod folder called @ISLANDS and for example units, vehicles and weapons i have @GEAR, and AI enhancements i have a folder called @AI.
I dont know how it works with servers yet but im going to set one up later. But cant the server have most addons in 1 single folder? Use SixUpdater or Yoma to get everything down easy and then have that extra folder you move everything new to. So in theory you could have 1 single folder you move everything into. Just an idea wich i dont know if it works with tons of *all* mods but so far when ive done it that way i never encountered any problems.