Both controllers support Raid. There are only two Gsata ports.
Chipset: Intel - (Blue)
- 6 x SATA 3Gb/s connectors (SATA2_0~SATA2_5) supporting up to 6 SATA 3Gb/s devices
- Support for SATA RAID 0, RAID 1, RAID 5, and RAID 10
GIGABYTE SATA2 chip: Gsata - (White)
- 1 x IDE connector supporting ATA-133/100/66/33 and up to 2 IDE devices
- 2 x SATA 3Gb/s connectors (GSATA2_6, GSATA2_7) supporting up to 2 SATA 3Gb/s devices
- Support for SATA RAID 0, RAID 1, and JBOD
I would connect everything to the blue ports. Leave the 2TB connected setup the raid with the the 2 - 1TB drives on that controller.
Plus make sure you set the Gsata controller back to IDE. You will have to setup the raid & re-install windows on that controller
Make sure you have that preinstall driver for that raid controller too. It is not the same as the Gsata controller.