If you know the specific fare class you want for each portion of the multi-city, you can use this code in the Advanced Routing box in Matrix. /f bc= then the fare class. Example:
AUS-FRA
AA+ /f bc=o
CPH-AUS
BA+ /f bc=t
Multiple fare classes can be specified by repeating the code /f bc= so I guess you could specify all fare classes for economy on the outbound, and for premium economy and business on the inbound.