*sigh*, let me look at the manual and see what is up...
I looked at the manual (starting on page 89) and didn't see anything worth mentioning outside of the normal process to install a RAID array which I assumed the OP already knew since he has a RAID array setup already. The Gigabyte ports are the White ones and support R0,1, and JOBD, while the other are the blue and I believe support the same or more (not sure).
So basically, you have TWO controllers to which I believe you can set each independently as AHCI/IDE/RAID. The Giga (which is what I said to install your SSD on), and the other controller (where you put your RAID I believe and are having issues). Now, if your RAID array was on the Giga controller initially, you will have to keep it there and put the SSD in the blue ports, or break the array and rebuild it on the other controller as you cannot take that RAID array intact to a new controller.
I hope that helps a bit. But definitely check out the manual for help if you need it. Here is a link from the giga site instead of a potentially questionable 3rd party link...
http://download.gigabyte.us/FileList/Manual/motherboard_manual_ga-ex58-ud4p_e.pdf
EDIT: So let's start over. You are breaking the RAID array and going single SSD, right? Do you want to use the mechanical HDD's as individual drives now? What will you be doing with those?
EDIT2: OK, reread the thread... you will need to break and rebuild your HDD RAID array (and will lose the data) if you switched it from the Giga ports to the other(blue) ports. You cannot switch controllers on a RAID array without breaking it. If you dont want to/cant break the array, move it back to the Giga ports and setup the SSD on the other ports (you should put the SSD on the Giga ports for best performance, note).
So basically...
If you do not want to break the array, put the HDD's back on the SATA ports they were on in RAID mode and the SSD on the other controller in AHCI mode. If the RAID array was setup on the giga ports, your SSD performance will be lower than with it on the Giga ports. To that end, I recommend putting the SSD on the Giga ports in AHCI mode, breaking and rebuilding your array on the other(blue) ports of course in RAID mode.