SuperDuper is missing a key feature - the ability to read and backup the files in the current user's home directory even if the user is using Apple's FileVault feature. It should give two options: Option one should be to mount the spare image on the backup drive and do a smart update to it. Option two should be to write directly to the backup volume and turning off FileVault on the backup volume (presuming you're using FileVault because you carry your machine about with you during the day but you don't carry your backup drive).
SuperDuper can't do either of these things but you can sort of approximate option 2 by backing up in two phases to two different volumes. First backup the entire disk minus your home directory and your sparse image (stored somewhere like /Users/.tom/) then backup your home directory to another disk/partition. If you end up booting from the backup, obviously your home directory is going to be missing (or rather, it's backup up to another volume) so you'll want to create at least one non-FileVaulted account that you can log into and recreate your home directory. Actually, you could even alter the backup system so that it sees the home directory backup as your home directory. Then you don't have to do any copying/fixing to get up and running again (at least until you want to restore your internal drive). You could get SuperDuper to run a script after backup. Something like this:
nicl -raw /Volumes/SystemBackup/var/db/netinfo/local.nidb \
-create /users/tom home /Volumes/HomeBackup
nicl -raw /Volumes/SystemBackup/var/db/netinfo/local.nidb \
-delete /users/tom home home_loc
I tried this and it seems to work. The only odd thing that happened was that after rebooting my "HomeBackup" volume was set to "Ignore Permissions" which I had to then switch off in the Get Info window.
