Although I've never dealt with this personally, I have dealt with similar issues where the thumb or pinky is playing a melodic line while the rest of the hands plays accompaniment.
When players are first learning how to play a moving line with the thumb or the pinky, we often teach them to lean their hand in that direction. Thus, if your right thumb is playing part of a melodic line while the remaining right-hand fingers are playing chords, envision leaning the hand to the left so that the emphasis is placed on the thumb. (You'd want to lean the hand to the right if you want to emphasize the pinky.)
Of course, this brings with it some timing issues that you'll want to work out: the lean may create a problem where the thumb articulates before the other fingers, so this is where personal practice comes in to alleviate that problem.
So to answer your original question, I'd say to follow the natural anatomy of the hand. Since the middle finger is the longest finger, try leaning the hand forward (towards the finger tips) to give the natural emphasis to the middle finger. But as above, this is only a starting point; you'll need further practice to address any ways in which this affects your tone and timing.