Hi,
1) I'd defiantly use the Intel sata ports , they offer the fastest raid option, also using Matrix raid gives you mre options for example you can run 2 stripes 1 raid0 for your OS - Fastest & a 2nd raid 1 or 5 i(with 3 drives)
2) You can also run with stand alone drives. I usually run with 4x80gb matrix raid as described in 1) , then with 2 further 500gb drives which though running under raid mode are stand alone drives.
3) as you add drives you can just use windows disk management utility see admin tools. to initialise & format the new drives.
Raid GuideBuild Guide Gigabyte X48T DQ6 luck:)