I put two 2TB drives into a Raid 1 array in the 2x Intel 6Gb/s ports, installed windows, installed the latest Intel Rapid Storage Technology so as to utilize my 128 OCZ SSD put into a Marvell 6GB/s slot. RST would not recognize the SSD from the Marvell port though I could see it in disk manager. So I put the SSD in an Intel 3GB/s slot, and it appeared in RST, yet the option for setting up Smart Response was not listed along with 'Status', 'Manage', 'Preferences', or 'Help.' Also, The RAID array is apparently "initializing" according to the software, so I'm thinking that that may have something to do with it. What is going on? Am I going to have to switch the HDDs to the 3GB/s and put the SSD in the 6GB/s? My HDDs are 6GB/s drives, and I have 6GB/s cables. What should I do?
I suspect that the reason you are having trouble with the setup that you're describing is because the ports use different controllers. I don't know all that much about iRST but I wouldn't be surprised if it won't work with the Marvell ports.
Your best performance will come from putting the 2TB drives on sata 3GB/s ports. Some hard drives claim 6GB/s compatibility but in reality not even the fastest mechanical HDD's are going to come close to even 3GB/s speeds because they are limited by the RPM of the platter. So even though they are technically 6GB/s drives you'll see no performance difference on 3GB/s drives. On the other hand, your SSD will be much faster on the Intel 6GB/s ports than it will be on the Marvell 6GB/s ports.
Now, what is your entire hard drive setup? Is the RAID1 your boot drive? If it is then the best performance configuration that you can get from those three drives is to install your operating system on the SSD and to use the RAID1 for mass storage. That's what I do and it works great. If you decide to boot from the SSD, the port configuration I described earlier would still be the fastest configuration.