I was wondering is their a procedures to Chang the coolant in 04-08 5.4 engine?
Or I just drain and refill from the over flow tank.

 

...can't be certain about your ride, but the scheme for replacing coolant in a 4.6L (nearly the same as the 5.4L) engine in my Lincoln TC recommends removing the heater hose from the port at the back of the manifold and then filling with new coolant until that port starts to overflow. The hose is then replaced and the refill completed at the overflow tank. The reason for this approach may be to ascertain that no air is trapped in the engine cooling system that could lead to temporary hot spots when the engine is restarted.