Thought I'd bump this up in case anyone is curious how it turned out. Certainly my scenario of one SSD and one or two RAIDs must occur frequently, so maybe this can be helpful.
In a nutshell, to run one SSD drive with Windows 7 (or
, 1 optical drive, and two RAID1's (or RAID0's, etc.), starting from scratch do the following:
1) Connect optical drive to port 4 or 5, and connect SSD to port 0. Boot to BIOS, set SATA ports 0-3 to RAID, and set SATA ports 4-5 to IDE (temporarily). Individual drives work in RAID mode as single drives unless they are assigned purposefully to a RAID. Have proper RAID drivers from Gigabyte CD copied to a USB stick and insert in one of the USB 2.0 ports.
2) Assuming all other BIOS settings are correct and PC is assembled and ready for Windows, save BIOS and reboot, allowing PC to boot from Windows disk. When Windows installation asks for drivers, browse to your USB stick where it's stored. Install will proceed from there. After install of Windows, install all necessary drivers from Gigabyte CD, then turn off PC.
3) Move optical drive to SATA port 1. Reboot to BIOS, change SATA ports 4-5 to same as ports 0-3 (RAID). Finish boot to Windows to check function of optical drive, then turn off PC.
4) Connect drives to be used as first RAID (I put two 3TB drives on ports 4-5, and two 2TB drives on 2-3, but only do ONE RAID per boot!). Power up and before boot completes, and while RAID BIOS is scanning drives, hit ctrl-f. Follow procedure to setup RAID's (see manual or ask here, I'm now somewhat competent in this!).
5) Boot to Windows and go to Disk Management, it will immediately ask you to setup the new logical disk (RAID) with a partition scheme (MBR or GPT). I used MBR for my 2TB RAID, and GPT for my 3TB RAID. Please note MBR partitioned RAID1's seem to be separable and readable as individual drives, but I was NOT able to view my GPT partitioned drives as individual drives on another PC. Right click bar representing new RAID logical drive and make new simple volume. Format, then check functioning.
6) Repeat from step 4 for second RAID if you're filing up the SATA ports like I did.
Someone let me know if I left something out here.
So yes, Gigabyte motherboads with 6 SATA ports can have an SSD, an optical drive, and two RAID's, all at once. Back when I was first researching this, I emailed Gigabyte tech support via their website, and THEY ARE IDIOTS. I asked if I could do exactly what I ended up doing, and the response I got said no, AND WAS WRONG ON EVERY POINT! Want some fun? Here's the actual response I got when I asked how to do this:
"Dear customer,
Unfortunately configuration you have not able to be supported on 990FXA-UD3 board. Board support Raid mode or AHCI mode not both at the same time and single Raid array only not 2. Board using software Raid, Raid array capacity has limitation up to 2TB.
You can set single Raid configuration on SATA port 1-3, connect optical drive to port 5 set to IDE mode, load OS to Raid drive first install all drivers, then change port 4-5 to SATA mode, connect SSD drive to port 4 that SSD drive will works in SATA mode.
Best regards,
Gigabyte technical support team."
Wrong about EVERYTHING! HA! Unbelievable... :-P