My baby came home to us at 7 1/2 weeks because the breeders were friends of ours. He was ready to go and has done great here.
If I were gone all day, I would do the same thing you are doing now. Giving him his own space with a pee pad. I think it would be miserable for a Yorkie to be in his crate all day. Especially with as fun loving and adventurous as Yorkies are, you can imagine how they feel about it. I crate train and aside from nights, the longest I have left my yorkie in his crate is three hours. I have a friend who keeps her Yorkie in a crate all day and she has behavior problems. We call her spawn of satan.