The main thing is that it just takes time to develop a repertoire. Your repertoire will never be perfect - there will always be some opening your opponents can throw at you that you're not ready for. But if you start playing a particular openings, for instance e4, you'll see the same replies often enough to know you need to spend a little time on them.

You play e4, and you know you need a line against the French. So you spend half an hour looking over one response, and you play that for a while. After your games in it, you can compare your play to how the masters would play it, using MCO and/or a database of master games. And of course, there will always be lines you're not ready for even within the lines you chose. You learn as you go.

The key is not to get overly worried about the holes in your opening repertoire. Plug the biggest holes, and don't try to make it bullet proof. It never will be.

--Fromper