I decided my best option was to drill the sump and hard plumb the skimmer output, making the drain section large enough for the drain, bulkhead and feed pump (5").
With 2 pumps, I initially thought I would use my Eheim, rated @ 607 gph for the skimmer and my Rio 2500+ @ 700 gph for the return.
After talking with tech support @ ETSS (AE Tech), they convinced me to use the Rio as it's a pressure rated pump, and ideally a Mag7 (which I'll do when I find a deal on one). According to them, a downdraft skimmer is different in the head pressure it creates and the Eheim, although a great pump, would yield less than spectacular results.
With some research, the Eheim return with the Rio feed seemed to be a good combination. The general concensus is to feed the sump about what the skimmer can process, and in this scenario the return would be approximately 420 gph (RC's head loss calculator) and the skimmer will process 350-400 gph.
Back to the sump, my design was, left to right:
5" drain/skimmer section
3 @ 8" bubble trap baffles
Middle - fuge
4" fuge baffle, later supplemented with 8" of eggcrate
5" return section
The last baffle height, for the fuge, was derived by creating maximum evaporation volume (ended up @ 4.5 gallons) but still being able to contain the 1.5" of sand I planned on using in the fuge. I added eggcrate to the fuge side of the last baffle, @ 8". to contain whatever I ended up growing in the fuge but still allowing volume fluctuations.
I chose 8" to get the most sump volume in normal operating conditions. I could have gone more with a 12" height on the 20l, but the maximum sump depth for the skimmer is 7". I raised the skimmer 1" using some wood that my light was packed in, 2 x 1/2" pieces glued together (screws were later removed) and painted black.
The issue that I ran into was the height of the skimmer versus the stand, and the need to be able to get the feed off the skimmer to clean the bio-balls used for bubbles created in the downdraft. This prevented me from raising the skimmer more.