I found that when I subscribe on the computer and sync it does not give me the full control experience that I get when I subscribe directly from the iPad. I've deleted all my courses from the computer, turned off iTunes sync, and left it all on the iPad for now.
I'm not entirely happy with that, but I figure I can always download specific videos and content to the computer on an ad-hoc basis. I could even subscribe on both, as long as I don't turn syncing on for iTunes U. Use the iPad for tracking everything and viewing on the go, and the computer to just watch videos at home, with the bigger screen.
Might even work best that way, since I could make notes on the iPad in the course while watching the video on the computer.