Found endometriosis during surgery to remove cyst and polycystic ovary, taken injection to control it but affect my QOL. Is it ok to live with it?

Yes. Endometriosis can cause pain and infertility. It is not life threatening. So if the treatment is worse than the disease as far as quality of life is concerned, it is certainly fine to forgo the treatment. Other possible treatments such as birth control pills and DepoProvera are also options that may not work as well but might have less negative impact on QOL. Hope this helps.