Don't use the web GUI. Go to the BACK UP tab in the standalone application interface. Just below the SHARE tab there should be a button that says Advanced. Press that and it will bring up a file browser that allows you to select whatever parts of your filesystem (eg AppData) that you want to back up. If you want to sync a particular folder between computers, you have to make sure it is getting backed up first. Just don't sync your wallet like I did.