I'm no expert, as I prefer to run all my kit without an Aquaero, personally. 
From reading similar threads on the forum, it seems you need a USB connection to do the initial firmware update and the first config on the D5, but the Aquaero can monitor it from thereafter. 
For example: 
Seeking knowledge about MPS, Aquabus & USB
Ideally, you want both, so that Aquasuite can have a separate tab dedicated to the D5, but if you want to keep it Aquabus only you can do that once it's set up.