Quick answer is that you can only have one account number per itinerary, but you can ask them at the airport to manually change one or more segments from AE to MP or vice-versa. The challenge is they often don't do it right and everything gets changed even if you only wanted the number changed for one segment. It's then very difficult to go back and get segments re-credited to the correct program.

A better strategy is likely to credit to the program on which you want to accumulate the miles then show your credit or other benefit card to get the benefit you want.