You did not specify which Revision Number your mobo is - possibilities are 1.0, 1.1, 1.4, and 3.0. I looked through the manual for Rev. 3.0. Although that manual does not say so clearly, earlier Rev mobos did something I had not seen before. On some, IF you install more than 1 HDD, it will automatically assume you want them set up as a RAID array! I am NOT sure your mobo does this. If it is trying to treat the two large HDD's as a RAID array, it will fail because Windows has NO driver for this setup!
You also have not specified what OS you are using, but I'm going to assume it is Win 7 or 8, 32-bit.
Anyway, assuming we are following the Rev. 3.0 manual, see Section 2-6 on p. 45, where SATA setup is outlined. Set "On-Chip SATA Controller" to Enabled, set "On-Chip SATA Type" to AHCI, and set "On-Chip SATA Port 4/5 Type" to As SATA. This configures all 6 of your SATA ports to AHCI device type, the correct setting for SATA individual drives NOT in a RAID array. Ideally, your boot drive should be connected to SATA Port 0, and the others to Ports 1 and 2. You'll have an optical drive on another port, too. For now you do not need to use Ports 4 or 5. Further on see p. 47 where it says you should set "SATA Power on Port n" to Enabled for each port you are using, and maybe also set the Hot Plug option for each port. Now, check under BIOS Features (manual Section 2-5, p.42) and ensure that the boot priority settings are as you want them - I suggest your optical unit first, then your boot HDD, and NO other devices. Don't forget to SAVE AND EXIT to preserve your changes.
Now, Win 7 and 8 do have their own "built-in" drivers for AHCI devices so this should work, BUT the manual actually recommends that you install the "correct" driver for this mobo's SATA ports. That often is a good idea. The problem is that, to do this really right, it should have been done as part of the Install of your OS. So, we have two options possible. We'll look at the more complicated "right" way first.
1. IF you are willing to start over and completely re-install your OS, you can do it "right". To do that you should connect ONLY the one HDD you are using for your boot drive. You need to do a little preparation before proceeding to place the required driver(s) on a USB flash drive stick. See Section 5-1-2 on p. 71, assuming you're installing Win 7 or 8. Under Step 1 they tell you how to copy the drivers from the mobo's CD to your USB flash drive, to be used later. Then you put your Win Install CD in the optical drive, ensure the BIOS is set to boot from that, and re-do the Install process. As a very early step, you will need to Delete the existing Partition on your boot drive so you can start fresh with an empty HDD. Now, note Steps 2 through 4 on p. 71. At the right prompt in the Win Install process you get it to read the correct driver(s) from your USB flash drive and install them as part of your Windows. You then complete the entire Install process. When you're done all of that, then you can shut down and connect your other two HDD's. When you boot up, they all should be there. IF you have a problem still, go into BIOS Setup and make sure to check in BIOS Features to be sure the boot priorities are set right - don't forget there is a sub-menu to specify WHICH of your 3 HDD's is the real one to boot from.
2. Now, MAYBE you'd rather not re-do the whole thing. You MIGHT be able to avoid all that in either of two ways. First option, IF your system will start working properly with JUST the BIOS Setup configurations above, you could leave it that way and rely on the AHCI driver that Windows already has installed, and ignore what the mobo CD has. Second option might be to "install" the "proper" driver from that CD from within Windows. To do this, of course, you have to be able to boot into Windows. You say you can do that if only your boot drive is connected. So, set it up that way and boot into Windows. Now look at Section 3-1 on p.51, where it tells you how to install drivers from the CD. Since you already have your system working, you might want to simply choose manually to install ONLY the required 32-bit AHCI driver for Win 7 (see p. 71). This will put that driver on the boot drive so it can be loaded into Windows at all future boot-ups. Now you shut down and connect the two other drives, then reboot. That may get you access to all your drives. If necessary, re-check the boot priority settings.
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