Sync is configured in the Sync preferences pane, accessible from the OmniFocus menu.
I have a vague recollection that things can get confounded if your keychain gets multiple entries for MobileMe. It may be easiest to work one-on-one with one of our Support Ninjas to hunt this down.
omnifocus@omnigroup.com or 800 315-6664 or +1 206-523-4152