The OS for the unit is stored on the internal drives. I'm not sure if 3TB drives will work in this unit or not, it has not been tested in our lab.
In order to change the drives, put the original drives back in and boot the unit. Delete any RAID arrays on the unit. Shut it down and replace one drive, then boot it back up.
If the unit will let you format the new drive it should work. Just format the new drive (this will store a copy of the OS on the new drive) and shut the unit back down and replace the other drive.
After booting, format the second new drive. If it works you should be able to create a new RAID 1 and begin using the device. If not, you may have to look at using 2TB drives instead.