Not a problem!!! Here is what I would do.
When you make the reservation with Disney Reservations, just give them the flight number you and DD are on to have your luggage tags, etc issued.
After you receive your boarding passes and luggage tags, call DME directly and change the arrival flight and date for your DS and DH.
The reason for this:
The DRC folks really don't know how to list different flight numbers. They just can't get it right.
The DME folks get your reservation 60 days before your trip and then issue the documents.
The DME folks DO know their computer system and know how to list the different flights.
You will not need new boarding passes and luggage tags for your DS and DH.