In case you missed the message from the other posts, DO NOT place the sub on your case. Your hard disks are very sensitive and if your sub is thumping while your hd is reading/writing, you will have major problems. And I'm pretty sure your sub is not magnetically shielded.
In terms of sound quality, if you want loud bass, just throw your sub in a corner. If you're looking for quality, it'll take some time to find a good spot, but a good starting point is near a corner but leave at least a foot and a half of space from the walls. If possible, try to have the sub closer to one wall than the other.
It'll take some time to find a good spot, but keep playing those CD's and listen for smooth, extended bass.