Sounds like you're in luck with Working Copy, as they mention this as being the only (known) application supporting background-sync for specific directories.
Do you have to remember to manually trigger commits/syncing or can you set it to commit/sync automatically (e.g., after a short period of inactivity)?
I'm used to using a variety of editing software and then manually pushing my notes repo, so the lack of automatic syncing doesn't bother me. In fact, I prefer it. I've been burned by auto-syncing before and it makes me nervous.