to the question as posed:

I would put the 327 at the bottom.   Aside from the more frequent goes higher idea, the transponder buttons are at the bottom of the box, which makes them nearer the a/p buttons if you put the 327 on top.

other uninvited comments:

- on takeoff you won't want to be looking that far down for your engine info.  I would find a way to get it high.
- if you can engineer a way to hinge the panel for rear access it would be worth it
- failing the hinge approach, push/pull cables underneath panel are the bane of avionics techs.   If I had it to do over again I would stack them vertically somewhere.   It will look dumb and save you $$thousands.