Wow, you really have a lot on your plate. I hope someone here can give you educated advice. I have never had a situation like this; but I can at least give you my thoughts. I'm not sure how you would have different rules for the yorkies and the dobe without creating competition between them, and that could be dangerous for the yorkies as the dobe grows. How much do you enjoy having the yorkies jump on the furniture, and do all their silliness right now? Most of us treat these little guys different than we would other dogs. The training the dobe to the crate until he is housebroken is a good idea; but, I would not keep them seperated all the time for the jealousy reason, also dogs seem to help train each other. I know you will get it done, and I hope you get help here, there is always someone willing to give advice. Congrads on the dobe, they are really nice dogs.
