Do with them what you will generally means you can do anything to them that you want, but it will make no difference. For example: Do what you will with a rubber ball, it will always bounce back.

"do with them what you will" = "do whatever you want" Most children are resilient and tough is what the writer is saying. You can do almost anything, and if it's wrong, the children will recover easily from your mistakes. Usually when you hear "Do with them what you will," someone is giving you something and telling you that you can either find a use for it or throw it away. The giver doesn't care what you do with it.