Hmm, this is a tough one. Can I just ask, as another scientific mind, how you are planning to evaluate whether he prefers one to the other? Maybe that would help us get some ideas on how to safely keep them separated. On the other hand, considering the nature of your experimental question, I'm not sure it's possible to truly come to any conclusions without putting them together.
Perhaps you could use items saturated with the females' urine (separately) and see if he is consistently more drawn to one over the other.
I know this is a very important experiment, so you're going to have to make a big decision about whether you are going to let your mice breed. I recommend that you decide this before you get them. If so, there are many people here on the forum who could help you to prepare for babies.
OR **** I just had a brilliant idea***** try to get in contact with a mouse breeder in your area. Maybe they would be willing to let you borrow (or at least observe) the mice together. You could use mice that they were already planning on breeding. Then you could really get some legitimate results, and you wouldn't be stuck with babies.
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Six new rats