On climb-out we set "standard" when cleared to a flight level and we cross check our alts then. We then have another altimeter check passing FL100. The standby altimeter is left on QNH until approaching FL100 on the main alts, at which point it is also set to standard, prior to the FL100 altimeter check. On the way down, a similar thing. As soon as we have the destination wx/ QNH we set it on the standby alt. When cleared to an altitude we set QNH on the main alts, and do an altimeter cross check. Passing 10,000/ FL100 we have another alt check.
It seems to work. In addition to all this, in the Airbus the altimeter setting will flash at you if the two main alts are set differently or you are passing transition.
I think this pretty much solves the problem and I can't recall any problems.