Yea there is one set of RAID and one for normal SATA which will probably be RAID aswell but to a lesser degree.
You can make 2 disks and load the different drivers for the 2 controllers when you hit F6 yes, I did this with the VIA and Promise controllers on mine. It also doesn't matter on SATA which controller you use or which socket you use either, I would suggest using socket 1 on either of them tho.
The RAID will only kick in when you have 2 drives and an array setup just like an IDE RAID will only kick in if you set up an array, if no array is setup then it works as a standard controller with RAID abilities.
Hope this helps
Boardy