Whenever you add a new member to your home (dog, cat, human, etc.) all of the animals in your home go through a re-calibration phase to figure out where they stand in the chain of authority.
What you're seeing with your new dogs "bossy" behavior is her testing the waters - What can I do/not do? Who listens to me? Who do I need to listen to? She is asserting herself to see who challenges her.
Thus far, it seems like the puppy has no interest in challenging her. He's okay with her being above him in that authority chain - and that's okay. Some dogs are naturally more submissive while others can be naturally more dominant. In time, the two will stop "testing the waters" and live in harmony without fear. I can say from experience that trying to force a submissive dog ahead of a dominant dog in your authority chain is stressful for them, because it's not what comes naturally.
What you can do to help facilitate this transition is to try to spend time with both dogs at the same time. Help them see how they can appropriately spend time together, and figure out what activities both dogs enjoy together (fetch, tug, sitting with you, car rides, etc). As alpha, this also puts the power in your hands to dictate which behaviors are (and are not) acceptable as they get adjusted to one another.
For example, if you are trying to get both dogs to play with a toy and the older one snaps at the pup in a way that you are not comfortable with (a more violent or aggressive behavior), correct her. A stern, loud "NO." should be sufficient for this, along with some hand waggling and removal of the toy for a bit. This sends her the message that although your younger dog ran off and gave in to her behavior, you do not tolerate it as head of the house. Repeat as needed if she repeats the behavior.
Again though, this is fairly natural. I had a 8 year old husky and a 4 month old lab pup that went through this same ritual. The older dog was the more dominant of the two, so she would bark in his face if he intruded on her space. That's OK behavior. She's telling him to leave her alone, she's not interested in whatever he is doing. What isn't OK behavior is any sort of attacking, so as long as that's not happening, you're probably in the clear and things should mellow out with time.