I use sata 0+1 for the boot drive, 2+3 for storage/programs HDD, followed by 6 then 5 for optical drives. This leaves room to raid the boot drive or or a storage array.
Make sure you have the sata type set to ahci, sata4/5 type set to same as..., and sata6gb/s support enabled (which is the default if I remember right)
Install windows to the ssd with just the ssd & optical installed.