Ben Max - for not being puppy savvy you are right on with your response.
You should try to pick this pup up fairly frequently and in repetition. Mild complaining on the pups part can be ignored and she will learn it is a waste of her energy to complain. Nipping, growling and snarling will get a correction (don't go overboard though) and when she calms down then she gets released. She needs to learn that calmness wins - not tantrums.
Good that you are doing lots of massaging and hands-on work, but try not to bribe her every time. Treats are fine but don't rely on them as she can get to the point of only being good if there is a treat involved.
We aren't keen on 'time outs', they can calm a dog down in the moment but it is a slow way to teach, and she is not sitting there contemplating the behavior that got her into 'time out' like a child would. Better to simply give her an appropriate correction and go right back to what you were doing. She will start to see a pattern in your responses and LEARN what is permitted and what is not. You should always go back to the circumstances that created the behavior so that she is given repeated opportunties to make a better choice and when she does give her lots of soft, warm praise.
Love Them & Lead Them,
~Elizabeth & Doug
Dog Training the Way Nature Intended