the confusion is totally understandable, even for women who don't have endo and PCOS... in your situation, it's no wonder that you're feeling
Progesterone doesn't cause cancer. However, what you may have heard is that the women on the combination HRT called Prempro in the WHI study exhibited an increased incidence of breast cancer, whereas the women on Premarin did not. Premarin is a mixture of conjugated equine estrogens; Prempro is a mixture of Premarin plus Provera. No natural progesterone involved there.
Frankly, I would be more concerned about the Provera you're taking now than your DR's proposed combination of a low dose of estrogen plus progesterone, assuming he/she plans to prescribe natural progesterone. I used depo Provera for birth control for three years several years ago; I was diagnosed with breast cancer last year. Since then I have been using bio-identical estrogen and a little progesterone, and have been just fine.
You asked if you will have to use estrogen after your surgery. If you are having your ovaries removed, then without estrogen you will have symptoms of surgical menopause. Most women do decide to use estrogen in that situation, though those with endo histories might wait a while before beginning the estrogen, or, as your DR is proposing, add a larger dose of progesterone with it to mitigate the stimulating action of the estrogen on any remaining endo implants. Another option is to use other, non-hormonal meds to treat the menopausal symptoms and help maintain your bone density. In any case, it will be very important to work closely with your DR for a while after your surgery, to either balance your hormones or find a combination of meds that work for you.
There are some links to good articles on HRT and cancer in our Resources forum. To find them, just click on Resources in the banner at the top of the page, and then scroll down and click on Breast Cancer. Perhaps they'll help you decide what you want to do.
Good for you
for considering this difficult decision before your surgery instead of after the fact.
Good luck with the surgery!