Question re. "Copy New..."

[cooper.smithsta]

Hey all,
Here's my situation:

I'm hoping to use a 250gb ministack as a bootable backup drive for my 80gb macbook. I will e using the ministack as my boot-drive only occassionally and/or in an emergency. However, that it be bootable is my primary concern.

I know I can ensure the ministack will be bootable by creating a clone w/ "backup all" or "smart update". However, I'd also like to keep *extra* information on the ministack that won't fit onto my macbook (e.g., 95gb of music files; my photo collection, as it grows), and that I don't want to erase every time I want to synch up my macbook HD w/ my ministack.

I was thinking that I could simply use "clone newer" or "clone different" to do this--however, in the SuperDuper! manual, it warns that you should only ever use "Backup-all" or "smart update" if you want your drive/clone to be bootable. Is this really the case? I don't want to have an *exact* clone of my macbook--I want to keep all my extra/excess files, and just update all the system prefs, documents, that may change on my macbook over time.

I suppose I could re-partition the ministack, make one partition for storage and another for an exact clone, but that's undesirable for a number of reasons...

Is it really s important/essential for a drive to be bootable that you use "backup all" or "smartbackup" every time, thus losing all the files which may be different on the backup drive? Why?

Thanks in advance!
Cooper Smith-Stackhouse