
Applied control theory for embedded systems
It is less math intensive and more intuitive and aims at folks with a software background like yourself.
http://smile.amazon.com/Applied-Control-Embedded-Systems-Tec...
PID control is probably what you'll see in an introductory undergraduate engineering control theory course (which I haven't taken). I think you'd typically study the dynamics using numerical simulation and Laplace transforms. You might think about making a practical project (I made a PID reflow oven controller).
After that you're off to the races with State Space methods (e.g. Chen's "Linear System Theory and Design".) and you can think about problems like stabilizing a quadrocopter based on inertial measurements.