@iridescentFluid in Syncthing's settings, you can set a default directory in which to place new synced folders. So while the default is "bad", it can be configured to your liking.
I say "bad" because you actually need easy access to Syncthing's data, that's its whole purpose. But I suppose ~/Documents/Sync or something would be a better default.
@yarmo I suppose I may be using it wrong, I really just want folder A to to have all the files folder B does. That is, I dont want new folders anywhere, I just want one folder to be a mirror of the other, like rsync.
I guess my biggest complaint is that the documentation is super confusing when all i really just want a quick and easy file transfer/sync app. It ends up being that each time i try to get that done, Syncthing just utterly confuses me since i didnt bother to memorize the GUI.