It really depends what you can or can not use. For example QFE operation is not allowed in our outfit anymore since we have EGPWS installed. That is in fact a restriction from the manufacturer of that system and therefore a restriction on the whole airplane.
We do use meters when operating on standard pressure (NG only, feet on the 733 with a table and a second stby altimeter in meters) and QNH/feet when operating below the standard level system. We are well aware of the differences, we do have to brief the difference between QFE and QNH well beforehand and all our charts have conversion tables. We do have to document all altitude/frequency clearances on paper and do a thorough crosscheck. For fast referencing the scratchpad of the FMC is quite a good place to store clearances. So far we didn't had any hickup with that.