Questions: Backing up 250GB to 1TB archive drive?

[Lornholio]

Hi, I've downloaded SuperDuper for my new setup and it seems like a nice program. I have a few questions on how to best use it for my purposes, forive me if these have been answered before - I couldn't find anything while searching.

I have around 500GB of files on my 1TB external archive drive. Files I am currently working on sit on my Macbook's 250GB internal HD and are regularly backed up to the external, and deleted from the internal once they are no longer needed for immediate use. I only connect my archive drive whenever I need to do a backup or search through old files. I do not work from files on the archive drive directly - they are copied to my internal drive and edited there. This works best for my workflow when travelling/etc. I hope that all makes sense.

So I'll be "backing up to a volume that has files on it" as detailed here. First question: will "copy newer" and "copy different" have the same effect for me? Which should I use?

If my internal drive does fail I can boot driectly from my archive drive, right? The potential problem I see here is that using "copy newer" or "copy different" will add and add to the system folders on the archive drive on every backup. Could this cause a problem if I was to recover from the archive drive? I'd have the system files and application data from last week backed up as well as those from months ago. Ideally I would want all my previous user files backed up but only my current system files, so a "copy newer" on the user files and an "erase then copy" on the system files. Is this possible? If not, would a solution be to backup all files with "copy newer" then manually replace everything on the archive drive EXCEPT the Users folder with those folders on my internal drive? Would this still be bootable?

...or would Time Machine do everything I need?

Thanks in advance to those who can help me here.