I have a hotswap bay on top of the case, an e-sata plug, a SSD and a HDD to hook up. Which of these should go on which MOBO sata ports?

I believe I have the Gigabyte UD3H. It has 2 Marvel controlled 6GB ports, 2 6GB ports, and 3 regular sata ports (I may have the 3 regular sata ports and 2 regular 6GB sata ports backwards as far as how many).

Also, should I be setting up some kind of raid?

I would put them on the lowers Sata port numbers. 

Nope dont worry about raid.