Ah, I see what you mean. In lieu of a 'saved sync' feature, which I'd like to add at some point, I think you'll need to set up a separate Bookmark to do the syncing from. Work/browse from one and sync from the other.
The Auto-Route feature is recursive, in that it will find all matches for the local path. If you don't want this behaviour then turn off the 'Recursive Auto-Route' option in the Transfers panel of the Preferences.