I was just reading an article aimed at live-gig engineers, the folks behind the mixing board at live music shows. There are some really good tips there and if you do live PA stuff, you should check it out. But one thing I took away from it applies to folks doing recording as well.
The not-so-obvious stuff is often the most important. And the one I have been thinking about a lot is that it does not matter if you know how to work the controls inside of Reaper, or Audacity, or Pro Tools, etc. Anyone can be taught how to pan and manipulate the mixing sliders on a track, or how to add effects to a track. But that is what we are trying to teach! We are trying to teach you how to produce great-sounding audio. For that you need to know WHY to do certain things, not just how. The how is usually pretty easy.
For example, if you know why to use a compression effect, and what can happen if you overdo it, then you can do it no matter what program you use. The Same thing for EQ. Once you understand the principles behind these effects and controls, then you can take that knowledge anywhere, even into the live sound world. All you may need is for someone to tell you where the particular controls and effects are when you move to a new program, or even to hardware. And that is super easy.
Anyway, here is the original article I referred to focusing on the not-so-obvious things in live sound work - http://www.prosoundweb.com/article/not_so_obvious_its_about_more_than_sound/P2/