Not to sound harsh, but knowing that Scooby (male) is a "fiercely loyal dominant dog" why did you not do a trial meeting with the two off property PRIOR to bringing her into your home and getting attached. Introduction is so important. You do not mention her age, if she is a pup, had a previous owner, if she was with other dogs, etc. This may have been an existing problem with her or another male was a problem in her previous home. It appears that you need to socialize and train two dogs now, as well as spay and neuter them both.
That said, until you undo what you have done with the male, socialize and train the two, you most likely will continue to have problems. And even then they may never accept each other and you will spend your time keeping them separated or eventually re-home one when it gets unmanageable. But all you can do now is try. But I strongly suggest if your life style does not afford you to keep a watchful eye on the two and do not have the means to set up your home for them to be separated comfortably, return the bitch to the previous owner/breeder now! When you enroll in obedience classes or have a private trainer come to your home explain the situation and have him work with you on the introduction of the two.
The mounting is a dominance thing not sexual and she may have been the dominant dog in her previous situation.
Good Luck!