I've done something similar, where Its LAX-HKG-MNL on PE but say the HKG-MNL (due to plane availability) is only Y so the LAX-HKG, i'd credit it to my main FFP, AA, and the HKG-MNL, i'd credit it to CX MPO, since it has better value to me (including keeping the MPO alive) than crediting an economy seat to AA.
Typically if it was LAX-MNL, i'd tell the counter to credit the flight to AA first and the next leg to CX, while say if it was the reverse, MNL-LAX, i'll have them credit it CX first (if the flight is Y only) and the long haul to AA. Just doublecheck on your boarding pass.
Note though if you have a better status on one FFP over the other this may impact your changes for things like OP-UP.