I see you received a lot of views, but no help.
I am not well versed with this controller yet as I just purchased it, but I had sort of a similar question. I wanted to ensure that I could independently control both pumps even though they would be connected via the Aquabus Y cable. I was told to get the pumps setup properly I had to assign each pump a name/code and that to do so, I needed to connect both the usb and aquabus (at the same time), make the designation and then disconnect whichever cable no longer needed (i.e. usb or aquabus, depending on how you plan to control the pump). Not sure if this helps. Also, consider posting your question
Here. There is quite a bit of support on that forum and the link is to the Aquaero owners thread.
Let us know the disposition as this may help some else in the future.