i don't think the ports matter. i used the two top-right ports (one black and one red) just because they were numbers 0 and 1 (i think. i'm going strictly off memory here, which sustained a lot of damage when i was in high school
set the RAID in BIOS like i said, then reboot and hit Ctrl-I while you're in POST to enter the Intel Matrix setup. pick your two hard drives for the RAID array, set the options (i always use 128KB stripes, but there is an endless debate about which size stripe works best. i have great performance with 128K stripes though). anyway, just select those two drives and create a RAID0 array. then you can reboot and boot from your Windows CD. if you're installing XP, you'll need to do the F6 floppy method. if you're installing Vista, you don't need the floppy.