When you add a flight-duty (CDR Definition - type other, on acft) in the section Crew > Duties, you can now select an option 'CPT or FO (best). It means, that if a pilot has both CPT & FO ratings and he is added to flight-duty as 1st - Leon will pick the highest rating (CPT). If CPT function has already been assigned to the other pilot - a pilot added as 2nd will be automatically assigned as FO.
We have introduced this option, as previously when using 2 crew members with CPT & FO ratings, Leon was assigning both of them as CPT - now you can plan the whole cockpit crew.
It is still possible to select a particular function: CPT or FO (or any assigned rating) from the drop-down box, in the verse 'Function'