I don't think it's necessary to auto-detect iTunes. A button or menu choice labeled "Connect to iTunes" would work fine for me. Then iTunes could show up as a device and be treated the same way as you do the iPad today. You could start iTunes if it's not already running.
I'll enter an enhancement request.
Originally Posted by GRiker
Possible, but tricky as there could be interactions with other device drivers, for example if iTunes is running but you plug in a Kindle - who wins?
Please create an enhancement request. I need to make sure that things are relatively bug-free with the existing feature set before adding new features.
In the meantime, you could create a custom column 'Add to iPad' that would allow you to keep track of books headed for iTunes.