I disagree, people are saying raid is not worth it...but they have not tested the BEST raid controllers...anything less than the best 20% of the market are absolutely horrible cards and your onbaord would be best if bothering with raid at all..
I suggest you DO use raid..
ignoring budget...your best bet is a very expensive raid card (areca 341 based/3ware 9xxx) put the whole lot in a raid 0 or 5 or 10 (10 if you have unlimited money burning a hole in your wallet), purchase as much cache and a BBU for said card & Probably a online UPS..
make it a single array, partition it how you want...depending how you plan to run you can always use partition magic and stuff around with it I'm assuming that you mean you have 2 x PCI-Express slots left over AFTER your cards are in...and, I'm also going to assume they are 8x or larger lane so you can fit a good raid card.
if you don't go for a "reasonably" expensive card, your better off with no card at all depending how good your onboard raid is.
again, if you have unlimited money you would not use raptors, but assuming you were stuffing around, I'd probably put the OS on a 6 drive raid 10, put 2 x raid cards in both those slots you have and stuff around with what works best across the drives filling the remaining slots on each controller...then mirror the whole setup to another raid 5 fileserver somewhere else...