I've manage similar to the way referred to by serfty. I let them go to their own trips though (instead of unfiled), but for nested tickets etc it's a matter of copying itineraries to multilpe trips and then editing them to remove the flights not relevant to that trip.

This might be more painful though, cause you then may need to adjust the trip itself to reflect the correct dates once you've got all your plans in place.

More of my flights are independent, so its easier for me to do this and have most create their own trip automatically then have to deal with each one manually.