I partitioned my 40GB to 15/25 since i'm a Windows convert, I used to have all the personal files on the second drive so it's easier when reformatting. But after 2 years of mac using, I don't see a real need for reformatting. So maybe you dont need to partition it... When it comes to new os x upgrade, I still prefer a clean install it might be handy then. So in conclusion, I'm on the same boat as you. I guess the best way is to get an external bus powered hard disk and not formatting the internal drive.
I'd like to hear more from experienced mac users. TIA!