I have 10 week old female Boston, who is aggressive towards our 11 month old Bull Terrier. He is terribly curious and has not shown an aggression towards her. She however barks and snaps at him which gets him rather excited. He is quite rough and seems to be trying to get her onto her back which really upsets her.
Do I need to be worried, is she just afraid of him because he gets so excited, will things improve as she gets bigger and maybe less threatened, or does she just dislik him? She doesn't display this behaviour towards my sisters dogs.

She is just being a brat - and your other dog hopefully will just show her who is boss. It may be helpful to teach "leave it" so that you can stop them if you think things are getting out of control. Unless your bull terrier has bitten a dog before, I wouldn't worry about it. Just keep an eye on them and definitely don't encourage the behavior by giving her a treat to avoid your other pup. If she gets to wild, just be quiet, grab her and stick her in the crate. She will probably bark in there too, but yelling at her is not going to help. Just ignore her and when she is quiet praise her. You may want to look into reading "My Smart Puppy" by Brian Kilcommons - it explains all the behaviors and has a training DVD so that you can see how to teach the commands. Good Luck! As of yet, not worried about your other dog attacking, just worried about your puppy developing a really bad habit of barking.