This proverb is South American and, it seems to me, a very gentle way of saying that God knows how flawed we are. And yet He loves us, no matter how crooked our lives appear, because He also sees the spirit of good in every human heart. God knows it’s there because He put it there.
That said, I don’t think that God “writes on,” or uses, the part of us that is flawed. As Christians we call this part the old Adam or the flesh or our lower nature or maybe even our evil self. These are, as MacDonald described them, “an opposition” within us, the “part of [our] being where God is not” (Anthology 84).
God is really only concerned about the part where His spirit is, in our soul. MacDonald described this best when he said that God is working “behind our consciousness … coming forward through regions of our darkness into our light” (Anthology 47). That’s why God’s divine influence may not at first be apparent to others, or even to ourselves.