You should be able to have a separate FFP number entered against each flight. In theory. In practice many check in/call centre agents apply the FFP # against all flights on the itinerary. So there is potential for things to go horribly wrong.

When it works it is a neat idea - I do this on *A amongst several FFPs to maximise earning and status benefits, optimise my (re)qualifications, take advantage of arbitrage between FFPs, etc.