Currently, once you set up scheduled sync, the parameters for the sync itself cannot be modified, although the schedule periods can. This is something I'll be addressing in the next update of Yummy FTP.
For the problem with files going to the root directory, I did fix a bug like this already in a later build. It would only happen if your server dropped the connection during a synchronize, however, and even then it was intermittent.
Since you emailed me at the support address, I have already provided you with the latest beta version of Yummy FTP which resolves the upload error. If anyone else has this problem, please do get in contact: support at yummysoftware dot com
-Jason