My initial suggestion for backing up your boot partition would be to attach your backup drive, encrypt it with a good password, then perform your backup. This should (will be testing tonight) create whatever partitions are necessary. It will also create CoreStorage logical volume groups. Be careful what you do with this backup drive because the CoreStorage volume structure can be messy to fix. See blocked
http://arstechnica.com/apple/reviews...-x-10-7.ars/13 for more information.
To backup your boot drive, you'll need to mount the backup drive (connect it) and enter the encryption password to allow it to be used. You get a recovery key when setting up FV2 on your boot drive but I doubt this same key works with other drives you encrypt from your main computer. I also doubt your encryption keys will match between your boot drive and any external drive you encrypt. I know you can set up an encrypted Time Machine backup because I've seen the prompt for it.
Having SuperDuper! clone the recovery disk/partition shouldn't be necessary and might not work if cloned. If you hose your boot drive (I did once already), I agree with the other suggestion that you quickly perform a clean install of Lion then restore from your backup doing a Smart Update. If you just restore your backup to a clean disk, it won't create the recovery partition but this can be easily created by re-installing Lion on top of the restored version (did this today). I believe doing it this way requires you to redo your FV2 configuration.
I'm finishing the encryption process as I write and will look at the encrypted drive to see what it looks like. I might not be able to mount it without entering a password and I can't mount it on a non-Lion Mac (already tried). Once I enter the password, the disk is available for reading/writing so I won't be able to see what the files look like. From what I've read, FV2 is at a different level than old FV so it doesn't use the same sparseimage bundle. I'll check back when I've finished my testing. Wish me luck....
Saturday morning:
Finished encryption last night, formatted backup drive as HFS+ (case-sensitive, journaled, encrypted). This creates a non-recovery partition that is used for booting:
/dev/disk2
#: TYPE NAME SIZE IDENTIFIER
0: GUID_partition_scheme *160.0 GB disk2
1: EFI 209.7 MB disk2s1
2: Apple_CoreStorage Backup160 159.7 GB disk2s2
3: Apple_Boot Boot OS X 134.2 MB disk2s3
/dev/disk3
#: TYPE NAME SIZE IDENTIFIER
0: Apple_HFSX Backup160 *159.5 GB disk3
Ran SuperDuper! normally. First backup gave error on a cache file:
| 09:35:25 PM | Info | Error copying /System/Library/Caches/com.apple.Components2.SystemCache.Components to /Volumes/Backup160/System/Library/Caches/com.apple.Components2.SystemCache.Components of type 8 due to error 2
| 09:35:25 PM | Error | SDCopy: Error copying /System/Library/Caches/com.apple.Components2.SystemCache.Components to /Volumes/Backup160/System/Library/Caches/com.apple.Components2.SystemCache.Components of type 8 due to error 2: No such file or directory
Re-ran backup and it completed successfully. External disk uses FV2 encryption, requiring a password to mount it. This password can be saved in the keychain.
Saturday morning I restarted and booted off the backup. It came up with a different boot prompt asking for disk password. No problem, entered password and it finishes the startup. Once up, prompt ask for "any" password of my internal disk. I used my non-admin password and it looks like everything is available. I didn't try copying back to the internal disk. I restarted again and came back up under the internal disk. It did ask for an initial password before my PolicyBanner (search web for how to create initial banner) came up with the regular login screen. This initial logon is the same as for the external disk when booting, it unlocks the disk so you can use it.
I haven't done exhausted testing but my initial tests look good. The little hiccup is something I've seen on occasion previously and it didn't bother me after getting a full backup. FV2 works at the block level, not the file level, so things should work just fine. That said, you have to be careful when reformatting backup drives because once encrypted, they become part of a CoreStorage volume and this needs to be addressed before simply erasing the drive to make sure it doesn't affect your boot drive.