You need to configure it in OmniFocus on the iPhone, too. Go to the settings page, go down to the Synchronization section, and set it all up. Once you've made your selection of MobileMe, Bonjour, or Advanced, and entered the username, path, and password as needed, you should be able to go back to the Settings page, tap the Get Settings from Mac button and see the desktop show up when you click the Share Settings button in OmniFocus' Sync preferences, or do the email option.
What are you using for your sync method? Bonjour, MobileMe, something else? If you're using anything but Bonjour, you'll want to delete the client entry for the old client in the Sync preferences panel on the desktop version if you are no longer going to use that device.