Zak,
Again, I have been using SyncToy for three years now. Beta version is fine, but no reason not to stay with 2.0 for awhile. The best way to put it is it syncs EVERYTHING in the AC folder. There are five ways to sync, "contribute" being the safest.
As SyncToy makes the job of copying and pasting so much easier, you can always practice with it on another couple of folders and/or check the properites and make sure the total files, folders and MBs are the same.