Absolutely assert yourself as alpha, puppies need to know you are in charge and will learn from you, you don't have to scream and make a huge issue out of the peeing on you, however I would calmly take and control and teach the puppy this is not acceptable. You would be best to take control now while he is still young. In terms of confidence, it is difficult to tell from the little bit of writing whether he is confident or not, don't forget dogs will pee from fear as well - not that I think this is the issue here.
if your GSD is eating and eating and eating and losing weight - please consider testing for EPI.
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