I would make several short videos, then pick the best one (the most consistent one, likely).
You don't want to go longer than about 3 minutes or Jupiter's rotation will start to blur details.
I limit my AVI files to 2 minutes when I'm imaging at 4,800mm focal length, but that's not hand-holding the video.
Another option is -- especially if you're having good luck holding the camera in the right place -- is to go much longer and then use Virtual Dub to chop the resulting video into segments.
If Virtual Dub or a similar program won't accept the video format from your camera, look into a Snappy frame grabber. This is a hardware device that hooks between your computer and the camera and allows you to capture digital video to a hard drive. You'd then save the file in a format that Virtual Dub can handle.
UPDATE: I can't locate my copy at the moment (I'm out in West Texas at CSAC this week) but there's a good (if a bit dated) treatment of using video cameras for astronomy, called Video Astronomy. A number of "occultation chasers" use video equipment in their work, too. There is information about this at the web site of the International Occultation Timing Association.