If you look at this picture:
you see that in addition to the rear nozzle which is capable of thrust vectoring through basically 90+ degrees (horizontal and vertical) it also has a vertical lift fan (driven by the main engine) just aft of the cockpit which stabalizes the pitch of the craft. There are also roll nozzles toward the wing roots which stabilize, well, roll.
That flap(s) on top allows air to enter the lift fan when required.
As to your other point, the rear is seen because it's very hot, as compared to the fan exhaust. Both have very high velocities and volumes, but the forward fan jet (thrust) isn't nearly as hot as the combustion exhaust from the rear.