Yeah, 3m Nexcare bandages will flex better than anything else, which is what you'll need on knuckles. I'd just keep them lubed with vaseline or ointment (I like the anesthetic neosporin). From my own experience, the healing occurs beneath the wound, not on the surface. Anything you do to the surface should be to prevent infection and maximize comfort. If it can heal under tegaderm or toughpads, it can heal under a bandaid.
If they're really bad, you can get some of that tubular bandage stuff and cut a couple non-stick pads, coat with neosporin, and let the tubulars hold them on. You'll look like a burn victim though.
http://www.google.com/products/catal...ed=0CE4Q8wIwAA
Good luck -- glad you're able to post about it!