from what you say, it seems that you alreayd have your 40 gig hd as your primary otherwise you wouldn't be asking this question. It's not really hard to get your 80 gig as the primary with all of your programs and such on it and then having your 40 gig as your so called "storage". But personally i would do it the other way around. I would keep my 40 gig as my primary and then my 2ndary as the 80 gig. You only have so many programs and applications and it shouldn't really take more than i'd say 20 gigs of your space. So why not have your bigger 80 gig hd as you storage?
If you still want to go through with this, all you need to do is open up your comp and set your 40 gig as primary and set the 80 gig as primary. Then you need to reinstall windows XP on the 80 gig. If you have something on the 80 gig it's ok, but if you have stuff on the 40 gig as of now, then i would suggest reformatting the 40 gig hd. The OS that you might have pre-installed on it will take up space as well as all the other stuff you have on it.
I personally have a 60 gig primary and a 120 gig 2ndary, and for your computer to run better you wanna keep your OS running on a smaller drive but have less installed on it. I try to keep the least amount of stuff on my 60 gig as a i can and just use my 120 gig to download stuff to. Games, and other programs i keep installed on my primary hd.