My Boston puppy has eyes which go in opposite directions! I realize their skull shape affects this....but will she ever grow-into those eyes? Or will she always have the whites of her eyes showing as they are when you look directly at her??

when they're puppies they look more weird than when they grow up. my dog had that too and as you can see he has become gorgeus!

It sounds as though you are describing what is termed Wall Eyes or Easty Westy eyes.

As very young puppies sometimes you will see more white in the corners of the eyes but if there is still a lot of white showing after 4 months of age it will not get better, she most likely will always look like she is looking in both directions at the same time. This is a hereditary thing.