If God is wholly spiritual, and He made everything in his likeness, i.e., to be spiritual, He must not have made matter or be aware of a material world. Yet the Bible says He "so loved the world, that he gave his only begotten Son ..." (John 3:16). How could God send His son into a material world that He Himself is unaware of?
I remember wrestling with this question myself. The answer finally came in the form of this analogy: If a mother sees her child having a nightmare, she doesn't have to know the specifics of the nightmare in order to help her child. She just knows that the child is suffering without cause and needs to wake up.
The important thing to realize is that even though some points may seem more difficult to understand than others, one can still practice Christian Science healing effectively. Mary Baker Eddy, the author of Science and Health, said that what she'd discovered is a divine Science, whose rules of spiritual existence can be proved by anyone. "In order to apprehend more," she wrote, "we must put into practice what we already know" (p.323). Just as a person doesn't have to understand the laws of calculus in order to do simple math problems, one doesn't have to understand the whole of Christian Science at once. As I've kept this in mind, I've found that the answers to the tougher questions do come.