Do you expect finite beings to fully comprehend something that is infinite? If your answer is no, then you know you are using the "God is not the author of confusion" line way out of context.
First of all, that line comes from 1 Corinthians 14:33. Let's see what it says in its context: 1 Corinthians 14:28-33
But if there be no interpreter, let him keep silence in the church; and let him speak to himself, and to God. Let the prophets speak two or three, and let the other judge. If any thing be revealed to another that sitteth by, let the first hold his peace. For ye may all prophesy one by one, that all may learn, and all may be comforted. And the spirits of the prophets are subject to the prophets. For God is not the author of confusion, but of peace, as in all churches of the saints.
In the Greek, the word confusion is translated tumult, or unquietness. This verse is refering to holding your peace when a prophet speaks. It does not refer to us fully understanding the nature of God.