When I take my progesterone I have signs of estrogen dominance, but when I don't I get hypothyroid again, what should I do?

See endocrinologist. If your Progesterone levels are impacting your thyroid levels to that extent, you probably need to have an expert looking at your overall hormone picture. Your situation is one which merits special attention. Seek out a recommended endocrinologist.
Change dose? Consider cutting the dose of progresterone? Use a vaginal cream? Vaginal or around the vagina application of hormones is the best delivery system. A little goes a long way. You may need a compounding pharmacy to make it for you.