I was experimenting with a plane that had a deployable smaller plane (similar idea to this concept https://www.simpleplanes.com/a/4yIbtt/Deployable-Glider) and I found that when I deployed and controlled the smaller plane, the control inputs would also affect the larger one and sending it way off course. Activating autopilot also worked toggled for both the smaller and main craft, not one or the other.
Is there a way I could launch a smaller plane from the main one and control it while the main one maintains level flight?
You could hook the same AG that releases the smaller plane to a gyro that immediately puts the main plane in level flight. For added extra, only enable the smaller plane's control surfaces when the AG is activated.