I'd suggest these steps:
1. Put a new large HDD in the bottom tray of your raid unit.
2. Let the auto-mirroring from the top drive to the bottom one finish.
3. Remove the top drive.
4. Using partition magic 8, expand your "/" partition on the bottom drive out to the remainder of the unused space on the new drive.
5. Now put a new, large hdd into the top tray and install it.
6. let the auto-mirroring finish from the bottom drive to the top.
Don't know if this will work on your raid unit, but it should, Specifically, if step 2 works, you are home free, and you won't have to sweat over bad backups and restores.
Regards,
Tom