Lisa,
If you can live with "herding" your dogs, then things should be fine. If, however, you think that "things will get better," you are deluding yourself. Sure, there may be times when your female doesn't try to kill the pup, but that doesn't mean a bloody fight won't break out out-of-the-blue. Been there, done that,know what I'm talking about. When the pup gets big enough to defend himself, they WILL fight. Every single act of aggression will only make things escalate. Until you have seen two Akitas try to kill each other, you can't know what I'm talking about. Akitas do not "get over" their hatred of other dogs. Sounds like your female hates this pup. That isn't going to change. The only safe route is to keep them physically separated at all times. Sadly, that really isn't fair to the pup or to you or your family. All of your lives will be limited as a result. I don't mean to be so pessimistic, but I do think you should know what you're really up against.