I can see how it becomes more difficult if you have an easily excitable barker. I just feel blessed with mine. We're still working on her socializing/barking on walks at other dogs she doesn't get to sniff at. It definitely becomes a bigger problem when living in a place where you have to share your walls and possible hear complaints from your neighbours. I hope someone can help you with teaching the "no bark" or "hush" or "shush" command to your pup. It is a bit more of a worry too since you have a smaller girl but otherwise, I'd just let them "duke it out" on the floor before worrying about their behaviour towards each other on the bed. The puppy probably is barking out of fear and thinks it's safe high up on the bed so she keeps going at it. It's usually best to let the cat establish his alpha position above the yorkie and it doesn't usually get "violent" but to everything there are probably exceptions.
I wish I can be of better help other than to say that time will work things out between the two of them... only in your situation, you will get a lot of barking along the way.
