Hi,
This is the way we operate where I work:
After departure, when cleared to a flight level, we set standard on both of the main altimeters straight away, leaving QNH set on the standby altimeter until we have climbed above both MSA and transition altitude.
During the descent, while still operating to flight levels, we set QNH on the standby altimeter in order to monitor our position with respect to the MSA. When we get cleared to an altitude, we set QNH on the main altimeters.
Hope that answers your question.
BB.