I used the ports in order from 0 and up (0,1,2,3,4) and put the boot drive on zero and then installed Windows 7 without much fuss. About all I can warn about is to label what drive goes to what port to avoid finding out what happens when you mix them up later.
On my motherboard there are six SATA plug in locations. I was wondering if there is an order that the devices should be plugged like the IDE of old. I know there are no jumpers to set but just curious.