AHCI is a subset of RAID so it should work for your SSD (trim, etc.). Install Windows with only the SSD installed, do a custom install and use the whole drive for the system. Let Windows do the partitioning. Once installed do all the driver and windows updates and then add your RAID array disks (they can go on the 6gb ports), go into RAID setup and create the array. That should do it.
Perfect... that is exactly what I was looking for! So its ok for the HDD's to go on the other 6GB ports even though they are ASMedia controlled and not Intel? That would be good news for performance.