Not sure about online courses, but its worth reading some books! I would suggest "Designing Circuit Boards with EAGLE", among other books. The knowledge you acquire from this is not limited to Eagle, but to any CAD for circuit design. This may cover general needs on micro-controller stuff.
If you are aiming particularly on high-speed signal design, then you may need to read few additional stuff, such as impedance matching, EMI effects etc which can play a big role messing a PCB design in terms of signal quality, timing, cross talk etc. That would cover mostly on scholar articles, reviews etc., which drags you more into academia.