I had the same problem yesterday didn't know which option to choose, but then I read that the Omni Sync Server just uses WebDAV.
Therefore on the iPhone just do the following:
1. Open the OmniFocus Sync Preferences.
2. Select the Advanced (WebDAV) option.
3. In the Location field, put in your sync url.
https://sync.omnigroup.com/yourusername
4. Click the Sync Now button. It will then ask for your username and password.
That should be it, worked fine for me.