I've never owned a small breed, however GSDs can get on really well with small dogs. My female loves little dogs, she is excellent with them, will get down to their level and is very gentle with them - she loves little ones. I'm sure your puppy will be fine with your Yorkie, as your pup grows he will go through that interesting adolescence stage where he will start to test and try your authority etc and will test the Yorkie, however if you provide training and consistent rules for all, they will be fine.
if your GSD is eating and eating and eating and losing weight - please consider testing for EPI.
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