I see no problem with your setup. I was running a similar setup before I moved the RAID5 array off to my HTPC/NAS.
Most importantly, can I boot from the SSD while having a RAID array attached on the same controller? What would I have to set the BIOS to, AHCI or RAID?
You would set it to 'RAID' in BIOS, The standalone boot drive (your SSD) will be listed as standalone when Matrix RAID is doing its drive detection during POST.