I'm confused as to how the flaperon function impacts the use of dual elevator channels.

If anything you may need to TURN OFF flaperons and insteadl use a mix from the primary elevator channel to the gear channel, then reverse the gear channel and disable the gear switch ( so it doesn't screw up or affect the elevator connected to the gear channel ).

You could also opt for a reversing servo harness ( worst choice in my opinion as they "drift" with temperature changes ).
You can use a regenerative device like a Matchbox or the Futaba MSR... ( a good but costly choice as each cost about $70.00 )

OR you can merely reverse the horn position of one servo, so that servo one horn points up, and the other down... then connect both servos to the same channel... ( cheapest solution and quite effective ).

For this you'll have to assure that when you set up the linkages they are both "square" to each other as well as the linkages, otherwise you'll get dissimiliar movement.