I have had that set up before. Set up your non-RAID disks on the Intel SATA's, 1 & 2, not the orange plugs. Put your RAID on the SI plugs 5 & 6. In BIOS set the intel controller as non raid. SI set as RAID no boot rom. You will need to set the boot drive also. Let me know if you need the specific BIOS settings.
The two orange plugs for the quick raid are actually 1 sata plug split into two. Good for the n00b who wants to play with a RAID 0 or have the safety of a RAID 1, but not very efficient. You can also get a esata cable and use the other plug in the back.
The most I had on my system was 2 RAID 0's, the first with three drives on the Intel, the second with two drives on one SI, and a scratch drive on the esata.