Sean,

The transmitter/Receiver does not need to be set up for dual engine control though everything does depend on your choice of controller/transmitter. If you buy a 2 or 3 channel "trigger" type controller like those seen in use for surface boats or cars then you're in trouble and you have to be extremely coordinated to operate all of your channels. Especially for a sub. If you buy a 4 or 6 channel stick controller, things start to look up. Most stick controllers are set up to have a rachet style throttle control on channel 2 and the other 3 stick channels are spring return to center. This can be changed and you can set any of the other channels for rachet control(I would recommend the other vertical stick). Once you've selected which channel you wish to change, plug the other ESC into that slot on the receiver and you have dual throttle control.

simple no?

Dan