When commanding the sub with ManualCommand of Mavlink protocol, let’s say we set the x or surge to positive value in vectored-6dof configuration, why the motors that only move are at index 3 and 4? Isn’t it more efficient to also to make the motor 1 and 2 have backward thrushter? I am curios of why the current implementation only move the thrushter 3 and 4 to surge?
Hi @Lexciese, welcome to the forum 
ArduSub’s VECTORED_6DOF frame does in fact use motors 1+2+3+4 for all horizontal movements (surge/sway/turn) - the thrusters are bidirectional so the “backwards” ones just spin backwards to push forwards.
There are slightly higher thrusts when the thrusters are oriented in the direction of motion (as opposed to reversed), but how you physically orient your thrusters is up to you - we just recommend a symmetric approach because it’s more manoeuvrable when moving in arbitrary directions (as opposed to prioritising forwards over backwards, for example, which you could choose to do, or you could angle the thrusters to prioritise surge over sway).
How did you determine this? If that’s what your thrusters are physically doing then you likely have a hardware or configuration issue. Have you tried testing each of your motors?