As we learn more and more words, the readings come along. The more words we learn, the more we recognize the characters in words we don't know yet as "Ah, that's the one that's in ____! Then it's probably pronounced as __" and so on.

I don't think that there needs to be any particular way of learning readings, just accumulate a lot of vocabulary through a lot of your sentences or Core cards or both, whatever, and read a lot to reinforce it. Though you could have a look at things like the Movie Method or Kanji Town and see if you like them.