Looks like you've solved it already. You're right, SubFolder clauses do not currently work with Synchronize. (Synchronize only considers files, in a nutshell.)
Full Path or Location clauses are the correct thing to use for the Synchronize tool.
If you don't need the interactive aspects of the Synchronize tool, you could use the Copy or Copy Update All commands instead of it, which can be used in conjunction with a filter to restrict which files/folders are copied. SubFolder clauses will work there, and will speed things up if there are a lot of things in the skipped folders. See How to filter items by location or sub-folder and Filtered Operations if you want to learn more about that approach, and shout if you have any questions.