Your 3 month old pup is not being 'dominant' - she's being a puppy! Some dogs tolerate pups behavior well, some hate puppies. She won't be a puppy forever! She will grow out of the puppy phase soon enough. For now, give Winnie his own space when needed and put the puppy away. Have a place for him to get away when he wants to. You will usually know if he's had too much/enough or if he is enjoying himself. With time, I am sure the bond will grow. Don't overthink it.
