I have had a Biocube for a number of years so I can weigh in a bit. This looks like an older version of the biocube from the lid but I'm not 100% sure. Maybe the smaller version of it. I'm assuming it is.
The stock pump is okay for this tank, at best. My pump came with suction cup feet to make sure it stays down. Is that possible? Can you show us the two pumps? I say, use the more powerful of the two. The best way to increase flow besides getting a larger pump is getting rid of any 90 degree angles in piping and adding a third party flow fan.
Stage 1 on the right is gravity fed from the intakes. Add your skimmer and heater here. The CPR SR3 is a great way to hold media in this middle area, assuming it fits. Otherwise, Coralife has a media tray and charcoal filter designed for the biocube.
My recommendation is using either pump and UV
sterilizer in Stage 3 (left side). Stage 2, use SR3 with charcoal, de*nitrate, and rowaphos along with any kind of mechanical filter. Finally, toss in the biocube skimmer and a heater in the first stage.