(I've merged the threads, else someone might find one and not the other, and not see the replies.)
You can filter which sub-folders are Synchronized by turning on the Filter option in the Synchronize panel and filtering on Location or Full Path.
More about that can be found here:
Note that the "Subfolder" filtering is more efficient but, as the page says, cannot be used for Synchronize (at least currently). "Subfolder" is better when doing a Find or a filtered copy/move/delete, but not for a sync. Use "Location" or "Full Path" instead when synching.