How Is Endometriosis Treated?

I'm 32 years and been diagnosed with Endometriosis,in June I had an operation for cyst and blowing of tubes the doctor prescribed danogen-100 and Fertomid.For the first month I didnt have my periods it was just a small spotting chocolate in colour as a result I could'nt use the Fertomid because I was not sure whether I was on my periods or not.2nd and 3rd month I did'nt have periods at all and I'm taking danogen for the last time this month.Whats stopping my periods and what are the chances of getting pregnant?