Yup, on-board cheapo RAID like this depends on the OS doing most of the work, with the BIOS helping out managing metadata and bootup. You might have more luck getting 6.1 to recognise your arrays.
Personally, I would install FreeBSD as normal to a single disk, then do something similar to what's described at http://people.freebsd.org/~rse/mirror/
to get the base system on a RAID-1 slice sized to taste (which you can boot off without any special BIOS support); you can then do what you like with the rest of the space; gstripe, gmirror, graid3, gvinum, gconcat, etc.
I'd also be looking at a PCI SATA controller to replace the SiI 3114; Silicon Image controllers are renound for their bugginess which only the Windows drivers seem able to work around effectively.