Mark, you should use your common sense and just set everything up "dry-run", see how you like it ;-)
Kidding aside, the best thing is to just sit down in the middle of the floor with everything you plan on placing inside there. Tinker around with placement, location, idea's, etc. See what suits you, as the person who has to clean and care for all this, then try to see what it does to bubble problems, etc. Try looking at some of the commercial sumps available, see how they designed certain sections and why...
I've never fooled around with my sump too much after the initial setup, and been very happy with it. It's a 55 Gal tank that sits under my 90. I have two baffles in it, one in each corner. They basically wall off the back two corners, and create a trapezoid shape, with the front glass being the longer edge (full 48 inches), the back of the tank, is only about 36 inches across (and the baffles form the sides of the trapezoid). The two corner area's house my pumps (Eheim for the return, a Sen powers the line to my refugium which is on the Left side). I've placed heaters and other essentials back there without any troubles, as I've made raised platforms for the pumps:
That last one you may want to think about... as I learned it the hard way. Overflows inevitably plug, pumps will keep pumping, and I overflowed my tank, and drained the sump down to the bottom before. Since placing the pumps on a pedestal (old drinking glasses work great), (knock on wood), I haven't flooded, but have tested this mechanism during water changes... Water level drops in the sump, and runs the pump dry, before you've pulled all the water out. If you plan on keeping anything alive down there, they will appreciate your foresight.
- Mac