Hey Arwen
I used the cream on the outside only. My CRS told me to apply it like you would lip balm. I know some doctors instruct you to put it in the canal but my didn't (thankfully).
I know what you mean when you feel God's distance on the bad days but I am sure of one thing-He is there. One of my favorite teachers gave this analogy (Beth Moore). Think of you and God sharing an adjoining suite in a hotel. You each have a door on your side. His is always open-it is we who close our sides.
I have struggled too with feeling like maybe I have done something wrong and maybe if I am good enough God will heal me but I have realized that there is nothing we can do to ever be "good" enough because nothing could match the perfection of God. Once I let go of that it eased a burden for me. I know God doesn't cause things like fissures but he is able to get good out of all things.
But really, there is nothing like the ups and downs or chronic pain to make you question.