You obviously care a lot about you fiancee. You sort of answered your questions already. You need to be very open with each other about the pain she is experiencing and about sex in general.
Every relationship is different and there is no one best way to communicate.
I find that being completly open and honest about the sex helps a lot. There should be nothing off limits between you two. So when the green light is on she can just come up to you and tell you. This may take some getting used to if the woman is not used to being the sexual agressor. She has to be able to tell you and take the initiative when she is able to.