I just went through this myself yesterday with a pair of Seagate SD3000DM001 3TB drives. My plan was to use them in a RAID 1 configuration through the motherboard, but when I plugged them in, the motherboard only saw them as 800 GB drives. After a little research I discovered that the maximum drive size the BIOS will recognize is 2.2 TB and anything after that gets "rolled over," so what my motherboard saw was the 800 GB which was left over after the 2.2 TB was subtracted. This was explained elsewhere as a limitation of the Intel chipset used in the board. Bummer.
Things looked up, though, when I gave up on the RAID and just started Windows 7 (Ultimate). The disk management console saw the drives as 3TB but divided them up in to 2TB and 750 MB volumes, with the 750 MB volumes being inaccessible. At least I could use 2TB of my 3TB drives, which was better than 800 GB.
Things looked up again when I visited the Seagate website and discovered that their "DiscWizard" software can make it possible to use the entire drive on older systems. The trick, apparently, is to change the partition type from MBR to GPT. Even better, it turns out that the DiscWizard software isn't necessary to do this (see below).
None of this, though, was helping me with my original ambition of using the drives in a RAID 1 configuration (for redundancy). One possibility was using a utility like SecondCopy to periodically copy files from one drive to the other, but I wanted real-time mirroring. Happily, it turns out that Windows 7 (Professional, Enterprise, Ultimate) has a software RAID 1 mode that does exactly that. It's called drive mirroring and to access it you simply go to the disk management console and click on the drives you want to mirror.
To get all this working on my system, here is what I had to do:
1. Run "diskmgmt.msc" from the "Run" window
2. Right click on the drive designation (i.e. "Disk 1" -- not the volume, which is the striped horizontal "window" at the right that shows the drive letter) and choose a GPT partition layout (as opposed to the default MBR layout, which has a 2TB limit). This gives a single 3TB volume (2800 GB) for the drive.
3. Once that was done for both drives, I right clicked again and chose a mirrored configuration. Instructions for this are available here: http://www.howtogeek.com/howto/17926/use-drive-mirroring-for-instant-backup-in-windows-7/
So, now I've got exactly what I wanted: a 3TB RAID 1 configuration in my old Gigabyte motherboard. Works great for storage, which is what I wanted it for.
LF