Backing up dual internal drives with Time Machine

I attempted to install Windows Vista last night on my system SSD drive, which required moving some things around between my two internal drives. I've been successful in the past using Carbon, but Unix didn't like it this time and corrupted my home folder. So I wiped the system and plugged in my Time Machine backup drive, only to find that the system disk's backup restoration interface was showing that it only backed up the drive with the system on it.

My SSD backed up perfectly with a copy from 5 minutes ago. My HD's last copy was over 15 days ago, which seems like a completely arbitrary date to me. What prefs could have changed since then?

So I went ahead and restored both drives individually (with a mean face) and upon restart all of my backups had returned that were not shown in the system restoration window of the install disk, but was able to be restored manually through the time machine window.

So...questions:

1) Why does this happen?
2) How can I reliably back up both drives in the future without the need to do half on system disk, half on desktop?

Thanks for the advice

It's probably a good idea to keep the backups separate otherwise you'll run into the same problem as before. It may be easier to have two separate external drives for Time Machine use; one for the main internal drive, the other for the SSD.

I have my backups setup that way and it's much easier to keep track of everything and when doing a restore. External hard drives are inexpensive and can be stacked. I keep four external drives on my desk which I use for both Macs that I have.