Not really sure what you mean by this. rc_channels_override sets thrust levels - does this example work for you?
If you want speed control you can try to use the IMU values for that, but without an actual velocity sensor it might not be very effective. I was mostly thinking you could command a constant thrust and it would be “good enough” to keep things moving.
If your vehicle can’t move directly sideways in manual mode when controlled with a joystick then either you’ve got one or more thrusters configured/connected incorrectly (check here), or your frame configuration may be poorly suited to your thruster directions and weight and volume distribution.
If it works well with a joystick but not via code then your code is doing something incorrectly 
Yes, the first four arguments to the MANUAL_CONTROL message are x,y,z,r, which should be as described here.