To the OP, I'd second Yooper and say that as long as you're recirculating/stirring the HLT, it shouldn't matter from a heat perspective. You should take into account the pumping setup you'll need to get the recirculation going. With an output from the MLT at the bottom you've got a much better priming site for pumping, and I imagine that most people them pump over to the bottom of the HLT, just so that they can connect the top of the HLT to the top of the MLT. I've not tried it, but depending on the setup you might find its easier to pump from the bottom of the MLT to the top of the HLT, but I'm sure someone else has probably given it a shot.
As for the ball locks, I don't recirculate in my MLT but do in the BK, and while you don't need ball locks on both spots, it certainly makes everything easier. Even if you've got the output above the level of the wort at all times (so stuff doesn't leak out when disconnected), its nice to be able to close everything off just in case. I generally only use one for flow control and leave the other wide open until I'm done pumping.