You have to bind the misile's to either a key or a secondery fire button on your joystick(primary firebutton is proberly bound to lasers/multicanons) under options setup....
then you go into the right UI-panel and set the misiles to second fire button and normal Laser/multicanon with the first firebutton,
unless you want only to use primary firebutton for misiles too, then you'll have to setup misiles to a second firegroup all together and then you can use primary firebutton for both misiles and laser/multicanon and simply switch firegroup for when firing misiles or lasers....