I don't know much about PCOS either, but I do know that I have cramps between periods and the symptom is known as mittelschmirtz or "middle pain" and that sometimes spotting occurs with it. I have also gotten cysts on my ovaries now and again.
I agree that getting it checked into might be a good idea, but I think you are probably doing okay and just settling into a rhythm.
I can't really say anything more than to ask the gynacologist. PCOS isn't something I know a whole lot about, even though I suspect I even have some form of it. I only know that for a normal cycle there shouldn't be any brown spotting between periods. For a normal cycle, the brown discharge is usually at the beginning and/or end of the menstruation period. While I do hope you are settling down to a regular pattern, I do think it would be a good idea to go in for a check up.