I would turn it the other way around. Assuming the Dynon EFIS is your main flight instrument I would dial in QNH or QNE (depending on your altitude). Common practise is to always have the second altimeter set to QNE (1013.25hPa; 29.92inHg) but if you do not need an altitude reading in Flight Levels it's fine if you set up one altimeter to QFE.
But remember: Even using this practise you HAVE to change the settings. QFE and QNH are both depending on the local pressure and therefore change pretty often. If you are on a cross country flight you then have to change both altimeters to different settings in order to have a correct altitude and a correct height readout.
Also make sure that you always use the same altimeter for altitude and the other one for height so you won't use faulty values from the wrong altimeter!