Hi @lunarminer, cool application!
As @tony-white mentioned, ArduSub is not really set up to handle this kind of hardware - it would fall under the advanced control options that we’re aware of as ideas but haven’t yet been implemented in ArduSub[1].
ArduSub’s motor motion axis contribution factors are used to specify how much each motor output should change when processing commanded movements across one or more motion axes, or how they should be set directly when in manual mode.
If you’re able to assume your vehicle will always have some forwards thrust (or momentum) when it needs to pitch or move vertically, then it could be sufficient to specify motor 3 as controlling both throttle and pitch, although behaviour may not be optimal (it does seem worth a try, at least!).
If your vehicle sometimes needs to move backwards and vertically while operating in an automated/stabilised control mode then I expect ArduSub’s current feature set won’t be sufficient for your use-case, although it could be workable if that only needs to happen in manual or acro mode 
Using ArduPlane and pretending your movable mass is in fact a pitch-focused control surface is likely the closest you could get to properly designed control of your vehicle with an existing ArduPilot firmware. That said, using ArduPlane effectively underwater may require some modifications.
It currently assumes every motor is a statically-positioned thruster. ↩︎