Leave the pump where it is. You want it to continue working when evaporation lowers the water level.
Live sand is also a good idea.
Baffles serve two purposes: to keep the water level at a consistant height in earlier chambers, and to remove bubbles created by your drain line and skimmer. You could put a baffle in to keep the refugium seperate from the pump return chamber, but you'll have to be more regular about top-offs, as the smaller pump return chamber will show the effects of evaporation more quickly. If you do put one baffle in, you might as well do a bubble baffle set. (Force water over, under, over a set of three closely spaced baffles.) A space-saving measure that would keep sand out of your pump is a half-height baffle sourounding the pump. Sand should stay outside the baffle and not get into the pump.
Extensive write-up on sumps: