The directions of the motors depend on how the wires are physically connected. Because of this, configuring the motor directions in software is part of our software setup instructions.
It sounds like you may need to re-calibrate the joystick (not the autopilot IMU) in QGroundControl. You can do this in the Joystick tab of the Vehicle Setup page (click the gears icon).
Are you pushing buttons or moving joysticks? The joystick calibration (and mapping) can be done in QGC. Please follow the diagram in the upper right hand corner when doing the calibration.