Things like this just take time. Once your girl realizes that the new guy is there to stay she may enjoy having a new friend to hang out with! It sounds like shes had bad experiences with other dogs in the past so make sure to let her know that good things happen when the new dog is around. Take them on walks together, play with them together, treat them often when they are together, you get the idea.
Also, her just coming out of a heat could be to blame for her behavior.
Make sure, if he isn't already, to get the boy neutered so you don't have any unwanted pups.