You can find the cable assignment in the instructions for the Aquaero and e.g. the Quadro under Support -> Downloads.
Re-flashing would only be necessary if you want to use a second Aquaero as a slave; this is not necessary for other devices with Aquabus. Nevertheless, the USB connection should always be connected, as not everything can be addressed via the Aquabus and the devices without USB cannot receive firmware updates.
Yes some how forgot about manuals

Thx