My personal take on how I would have liked to learn econometrics is to learn the tools and then the applications. That might not be for everyone, but I find that approach to have some nice benefits. I prefer to learn tools and then find how I can use them properly rather than find a problem and look for a suitable tool. When you only know the hammer, everything looks like a nail, but if you have a toolbox you learn to apply the correct tool to the proper case. I would consider research design a whole different monster, and tackle that after you know how to use your tools. It is similar to learning proofs and solution methods in math. Only after, you know how to frame and apply your tools to work various kinds of problems.