The BPK is a pretty good free template solution. I was a disappointed to see that their latest, BPK 3, is still a set of separate files. In my opinion, such an integrated solution should be all within one file, with multiple tables. However, if you wanted to work in separate windows (as they do) then a 1 file structure would present its own challenges. It would however work great if you wanted to only work in 1 window primarily.
You could, if you wanted to, rewrite the existing BPK to remain separate files, but still work within one file's layouts, that is, bring the layouts and scripts into one file, while leaving the separate files structure. But it would be better to bring all the tables into one file. I did that for myself, with BPK 2 (they later released BPK 3, but it's mostly the same), partly as an excercise. We had some idealistic idea (on fmforums) that we'd collaborate on extending BPK; but it never really went anywhere.
So, basically, you could rewrite BPK to work however you want to. But as a beginner I sort of doubt you'd want to.