What Is The Treatment For Ovarian Cyst?

Hello. I am 25 and have no history or pregnancy or serious medical issues but I do have a tilted uterus. Approximately 7 months ago I had laproscopic surgery to remove a 6 cm cyst on my right ovary. Prior to the surgery, my menstrual cycles were regular and only lasted 3-5 days. I am currently having 2 menstrual cycles each month that are not at all regular. A follow up sonogram showed a 4 cm cyst on the same ovary...apparently this is left over from the surgery. My doctor stated that she could only safely remove as much as she did. At this time she is not concerned that I will need a second surgery unless I cannot tolerate the pain and twinges anymore. She did mention that I either was not ovulating prior to the surgery or I am not currently ovulating. I am trying to conceive but this has made it extremely difficult. I guess my ultimate question is whether or not my menstrual cycle should be regular at this point in time. Is it likely that I am not currently ovulating? Should I seek a second opinion or would they simply remove the ovary this time?