Two solutions:
(1) As in MS FSX, the pilot flying presses a key command to relinquish control to the pilot not flying who must then accept control. Dual control, but not simultaneous. The roles are not fixed. When the PF relinquishes control and the PNF accepts, the PF becomes the PNF and vice-versa. This is a fairly standard procedure used in most two-pilot aircraft. Simultaneous control would be more challenging and not horribly useful (or realistic).
(2) Consider the A6 Intruder. If we take a look at its cockpit (http://farm5.staticflickr.com/4102/4928078520_a55600702a_z.jpg) we see at the B/N station a joystick, but it is not a flight control stick, it is a control for the targeting system. In this aircraft only the pilot has flight controls.