Two hard drives on 1 time capsule backup

So I popped my girlfriends hard drive into my MBP and wanted to back her files up to Time Machine because her computer died (not hard drive, just the logic board). Will I be able to write make two separate time machine back ups with my hard drive and hers? I tried and it started to change the name of "My Macbook Pro" to "Her Macbook Pro" so I canceled the backup immediately and put my HD back in. Now it is verifying my backup, hopefully I didn't mess anything up.
Anyway, the question is, can I do this by switching hard drives or is it using my network ID to determine which HD is connecting to TC?

That would work, but the backups would all be in the same sparse bundle, which would make accessing the right one a bit tricky.
Time Machine knows which computer is which, via a hardware identifier that's embedded in the logic board. It also knows which drive is which, regardless of the names.
So it knows that drive is a new drive on the same Mac. It will, of course, do a full backup of the drive, so may have to delete a lot of old backups to make room. If you have plenty of space, it will be ok.
Once the backup is done, you'll have to use the procedure in #E3 of Time Machine - Troubleshooting (or use the link in *User Tips* at the top of this forum) to view and restore from the backups of the HD that's not currently installed.
If both HDs have the same name (such as "Macintosh HD"), that will be a bit confusing. Rename the one that's installed by right-clicking it in a Finder window (a normal one, not in the Time Machine display). Then the list of volumes in the second sample of #E3 will show the changed name, so you can tell more easily which one was backed-up at any particular time.
And be sure not to run out of room for new backups; if space is getting tight, and Time Machine has to delete old backups to make room for new ones, it may delete the last remaining backup of the drive that's not currently installed.

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