If you want to run your RAID array you need to set the ports as RAID. I would plug the SSD into port 1, you should lose very little speed running the drive with the RAID controller in-lieu of the AHCI controller.
Did you run Sanitary-Erase before you re-installed Windows for the second time? Re-installing Windows over a previous Install will slow the drive down. Sanitary-Erase will reset the drive to it's original "out of the box" state. Here's a link to a good Sanitary-Erase Guide, it's from the OCZ Forum but it will work on your drive. Guide How to use Sanitary Erase
Here is my Guide for Tweaking your SSD once you get Windows re-installed
SSD Tweak Guide