mission commands are used to command the aircraft to waypoints. if you want to command the aircraft directly you should use velocity control. the other option, position control uses latitude and longitude.
for velocity control you use the SET_POSITION_TARGET_LOCAL_NED (or SET_POSITION_TARGET_GLOBAL_INT) MAVLink message. it controls the x, y and z velocities and is relative to the coordinate frame used (Local NED, Local Offset NED, Body NED, Body Offset NED). for example, MAV_FRAME_LOCAL_NED controls movement relative to NED where velocity x is north/south, velocity y is east/west and velocity z is up/down. the velocity is in m/s.
this example shows how to use Local NED and Global Int velocity control.