Ok I've re-read this post several times plus done a lot of searching in between my difficulties here and came to this conclusion.
1) Your SSD is a 6G
2) Your HDD's are a 3G
3) your CHIVF is being pulled down to 3G because of the HDD's even though your set for 6G.
Now the only fix for this is to go out and get some of these:
http://www.newegg.com/Product/ProductList.aspx?Submit=ENE&N=100007603%20600003483&IsNodeId=1&name=SA..., Your Choice. This will allow your 6G performance to come up to 6G of your SDD.
Now for the second part It doesn't matter a bit if you have all of your Ports set to Raid the Drives not set into a RAID will automaticlly drop into AHCI Mode and not Hard Drive Mode which is what you want.
I hope this is of help. I also have a CHIVF with the same basic setup but I'm running in 3G and no SSD yet(But soon). Thank you for putting up this question it has reminded me of another thing that I'm going to need to do when I get my SSD.