My rig is set up to fly sparge with one pump, and I have the MLT (orange) above the HLT (blue).
To make my system work w/ the one burner, I start my strike water in the kettle, and pump it up to the MLT once the temp is right. As soon as the mash is set, I start heating 5 gallons of sparge water, and when that reaches 175F, I pump the sparge water from the kettle to the HLT. It sounds like a lot of effort, but it really isn't once you learn how to prime the pump.
Bobby is completely right that it is a misconception that a pump should not be used on the output of the MLT for fear of compacting the grain bed. If that happens, it is user error. Throttling the wort on the way out of the pump keeps the lauter tun from compacting by draining too fast - it only drains as fast as you allow it to be ejected from the pump. When I am running my sparge, I do rely on gravity to drain wort down to the kettle, but I also run a 15 minute automated vorlauf through the mash tun as part of my mash-out routine. IOW, the pump is working fine be it pumping from the kettle, the HLT, or the MLT.
There is a big reason I like the MLT on top of the HLT. The reasoning is kind of the opposite of what Bobby said - I need to reach into my MLT to stir and measure temps, but the HLT does not need to have easy access. My system is designed carefully so that the kettle is high enough to gravity drain to a carboy, the MLT is high enough to gravity drain to the kettle, and the HLT is high enough above the pump to prime - but with those constraints in mind, it is as short as possible. My rig is only for 5 gallon batches, but at it's highest point, it is barely at my chest.