If you can control the power of both pumps when they are connected via USB and priority set to USB, then both of them should be ok, the problem must be with your connections to the Aquaero. Are you using a splitter to plug both of your pumps to the High Aquabus interface ? Also, before setting priority to the Aquabus, did you assign two different address to your pumps (12, 13) ?
As for the flow, it seems a little low, from my experience, the quick disconnect fittings are pretty hard on a flow rate, but still... What kind of fluid are you using ? Some time ago, I used some Feser fluid in a high restriction loop and I was having pretty low flow rate. The moment I replaced the stuff with a good old distilled water mix, i saw a big improvement in my flow rates (I can not tell how much since I only had a spinning wheel at that time to monitor my fllowrate, but the rotations seemed to almost double). Right now I'm running 187L/h with one EK Supremacy, one EK full GPU block, one 360mm rad (Feser), the AQ High flow meter (non USB) and two ugly QD3 with one AQ USB D5 at full speed (3/8 ID tubing for the loop). Before adding the two QD3 to this loop, I was hitting 210L/h...
Hope this help!