Well, I thought I would be pro-active and figure this out myself
I read about it a while, and then downloaded "HD Tach". I tried all different options and ran HDTach after each bootup. My results where almost identical - no matter what AHCI option I had enabled
So I am just going to leave them all off. Its still listed as SATA in PC Wizard and whatever, so I'm happy its all set up nice anyway Only other thing I could try, is putting it back into those other SATA slots instead of the (G)SATA ports and testing the speed in there. That will have to wait for some other time though.. I suspect its best how it is now anyway too.
And incase anyone is interested in my HD Tach scores, this is them (did lots so this is kind of average):
Burst speed:
1524.5 mb/s
Random Access:
13.5 ms
Avg. Read Time:
65.5 MB/s
CPU Utilisation:
2%