Irregular cycle...help?

When my husband and I were TTC our first I got pregnant within one month of taking myself off the pill. Our son will be three next month. I took myself off the pill 6/14. I had constant AF all the way unil I went to the doc. In October when he put me back on the pill and my first normal 28 day cycle was in February. The doc. Said I could go back off the pill and start TTC again. Now I have irregular AF and heavy spotting after BD. I have gone back to the doc. But he just put me back on the pill. But he said everything looks healthy minus I do get a lot of ovarian cysts. If everything is heathy how do I regulate my cycle besides taking the pill??