This may be obvious to everyone except me, but I found this by accident and it is useful for me. I’ve added Resources to my site from many locations on my hard-drive and the chance for something to get moved or deleted which I’m working outside of RW is pretty high. So, I used the “Make Document Portable” option in the General settings tab. That made my file really big (as RW warned it might), so it saved and uploaded slowly (because it was uploading a backup). So, I then used the “Unpack Portable Document” button in the General settings tab and RW created a folder that had copies of all my resources, previously scattered across my hard drive, nicely consolidated into a single place. In many ways, the best of both worlds.
Well, the best would be organization from the beginning, but barring that, this works extremely well.