I have had the same dilemma when thinking about converting a Garratt to DCC (see sig image below). The best solution it seems is to find one decoder that can handle the combined current from both motors. If you used two decoders, you can run them as a consist. But if the consist is ever broken you may have unexpected results. I've had consists that go wrong and I've had to reset the decoders - all a bit of a pain.