It's hard to really say where you should place them, as it'll depend on how your live rock is stacked / arranged. Generally, they are placed near the back corners or in the back half on each side. The point is to have no dead spots where detritus can build up and become a problem.
Ideally, you wouldn't want any air bubbles. There's really no need for any of the output attachments that come with the Maxi-Jets, unless you need to direct the flow with the somewhat triangular piece that swivels.