Hi @WiskiExplorers, welcome to the forum 
I’m a bit unsure what you’re envisioning here. If you want individual motor control you’d need 4 thruster commanders to provide the control signals to the ESCs. Assuming instead a more minimal control setup with just vertical, front-back, left-right, and yaw control (e.g. no pitch/roll control) you could link together give the same input signal to the ESCs for 4 vertical thrusters and control that with just speed control from a single thruster commander, and then link together a pair of horizontal thrusters on each side to control with speed/direction controls from another thruster commander.
With the thrusters there configured like in the BlueROV2 heavy
I would expect the signal would be cleaner (less electrical noise), and the wiring would be easier if the thruster commanders are in the same enclosure as the ESCs, since then you can use all four outputs of each thruster commander directly instead of needing to make multi-output wires, and the battery and power stuff can all be close together (which minimises power wastage). Since the control mechanism is just resistance-based it shouldn’t be a problem to have longish wires for that since very little current gets put through them. The 10kΩ potentiometers that come with the thruster commander should work fine on the other end of a tether (assuming it’s not too long), and you can even combine the ground and power wires.
That setup only requires six wires through the tether, so if you’re using a blue-robotics tether or other CAT5/6/7 cable then you’ll have a spare pair. If you don’t need that pair for something else then you can either leave it unconnected, or have the 5V and GND lines using a pair each instead of single wires.
Alternatively you could pair up the vertical thrusters (either front/back for pitch control OR left/right for roll control) and add in a wire to the vertical STEERING input, with an extra potentiometer at the surface. If you don’t have a use for the last wire then once again you can leave it unconnected, or you can put the GND through a pair instead of a single wire.
Note that the 5V and GND connections on the thruster commander are all connected internally (shown with thin lines), so you only need to join together one ground wire from each commander board, and one power wire.