Simply put... By tracking symptom frequency (i.E did the therapy lessen the patient's pain?).
Outcomes. If the patient comes in due to pain then improvement of pain is the goal, if she comes in for infertility then pregnancy is the outcome. I evaluate the patient looking for conditions that coexist with endometriosis and treat them all, looking for at least 50% improvement in the baseline pain scores. For the most part we accomplish that in 12-16 weeks after starting proper treatment.