
My girls when pregnant like to show the others of both sexes who is in charge, the humping is a dominance thing,nothing to do with sex, her hormones will be all over the place if pregnant or having a phantom and will soon settle down.
I agree that you should get both dogs used to being seperated now as you don't want her distressed during and post whelping or him whining the place down either, start by putting them in seperate crates in the same room, place one crate on top of another if space is an issue, nearer the time introduce your bitch to the room she is going to whelp in and get her used to sleeping in there so when she starts whelping it isn't strange to her.