I can't believe any one still uses QFE! Anyone flying A to B needs to know altitude or FL not height. All the charts, approach/departure plates, STARS etc. are printed in feet AMSL, all clearances are given in Feet AMSL (unless you're in China and get it in Meters AMSL!). If you have a problem subtracting aerodrome elevation then how the hell do you fly with QFE? thereby having to do a mental calculation for every clearance, arrival and departure? Even the GA industry who fly around the country in bug-smashers all need to be using the same reference altitude (or MSL) in order to safely communicate altitudes and call over reporting points.
The only advantage to using QFE that I can see is for the inexperiened pilot doing circuit training or similar local flying. It's simple to understand that when the altimeter says 0ft you have either landed or something has gone horribly wrong! Other than that setting QFE and flying towards rising terrain is positively dangerous (if you are relying on 0ft to be ground level) and then there is the problem of "Negative altitude" too.
Heavy jets have a radar altimeter (usually two) which, depending on the aircraft, comes 'alive' at 2500ft AGL. QFE is totally irrelevant, outdated, and in most situations very dangerous.
In response to the Altimeter setting question, ALL altimeters in the aircraft should be set to the same reference (be it QNH, QFE, or ISA), this includes the standby. When things start going wrong, confusion over the reference pressure for individual altimeters is not something you need to be dealing with.