With the rare delights of 2 altimeters, I revert to the KISS keep it simple stupid approach.
In short, I always keep both altimeters on the same setting be that QFE, QNH, 1013 etc. It allows me the joy of crosschecking at appropriate times, particularly during approaches.
Furthermore, you can only fly with reference to one so why add confusion by having them all on different settings. Using different altimeters just adds complication to the instrument scan, whereas it makes more sense to use a primary and backup method.
IMHO of course,
Obs cop