If I shoot two or three different projects on a P2 card, and I want to save my files off to a HD for use by my Avid, it seems like I have to bring in ALL of the footage on those cards, so that the "last clip" file and the file structure stays intact. Is that correct? Or can I just bring in the mxf files for one project, but not the others?
Always...always...ALWAYS back up the full card structure. I mean ALWAYS. That is your MASTER TAPE. Because you re-use cards you must always back up the full card. Back it up onto a drive you intend to archive. Don't import into Avid, and then delete the card. That's like capturing a tape and throwing the tape away.
AMA the P2 footage to access it from the card or card backup, then CONSOLIDATE the clips you want into the project. It will move the select few to your media drive.