Being an Aeronautical Engineer, i sought out the origin of this saying,

FLYING BY THE SEAT OF YOUR PANTS

Well, there's a pretty simple explanation. Before airplanes had sophisticated instruments and flight control systems, and even today, planes are piloted by feel. Pilots can feel the reactions of the plane in response to their actions at the controls.

Being the largest point of contact between pilot and plane, most of the feel or feedback comes through the seat of the pants.

If you are "flying by the seat of your pants" your are responding to the feedback received.