I would DEFINITELY get him neutered. That will help tremendously.
As far the situation -- when we first got Maggie, she attacked Franklin every chance she got. She was scared, in a new place with new people, new sounds and new smells. It is normal for them to not get along at first. The whole dynamic changes in a household when you bring in another dog and everybody just needs a little time to get used to it. I would keep the separate for a while - with us, I think it was 2 weeks? They were completely separate except for a couple minutes a day of supervised interaction. If one of them started to growl, we separated them again. We kept Franklin in the living room with us (where his playpen was) and Maggie stayed in the kitchen in her crate. At first I thought it was cruel leaving her out there alone. But then I realized she needed the time to adjust. To lay in her crate and learn our smells and voices. Once she was adjusted, we let them interact (again, fully supervised). Eventually they got along and today they're best friends!
Be patient and give them time. It's a scary time for both of the dogs. They'll come around eventually.
