There's nothing but God. If your "God is everywhere, but He is not everything" then your god is not omnipresent. You clearly have a mental image of God as a distinct thing or entity, which makes you an idolater and necessarily forces you to twist the actual meaning of the word "omnipresent" -- you presuppose that there is a "no-god", hence, your god is not everywhere at all times.

In any case, the answer to your question is God's omnibenevolence. As Isaiah 45:7 states, "I form the light, and create darkness: I make peace, and create evil: I the Lord do all these things." So, naturally, God is benevolent toward, and wishes well to, evil too. You know, love your enemies. Then again, there's no good and evil, just consequences and the same, identical I on the receiving end.

As I see it, if you had to choose between God and theology, you would choose the latter. In fact, you already did. Well, whatever.