I've done this about a million times now. First , let it cool all the way.
-remove the overflow tank cap.
-remove x-over tube plug ( on the driver's side of the motor, by the front of the blower....a 1/4 inch ratchet will open it)...all filling should be done here , as it is the highest point of the cooling system
-fill at x-over tube until overflow tank reaches fill level. Stop. Place cap back on over flow tank. Continue filling at X-over tube until full. I actually shake the car, you will see bubbles (read: air) come up. Some actually place the car on an incline or ramps. Place X-over plug back on.
-Set HVAC control to max. hot, start car and allow to idle until thermostat opens. (You can check lower radiator hose for heat to make sure it has), or allow the temp guage to come up to the middle.
-shut car off and allow to COMPLETELY cool.
-Remove x-over tube plug and fill agin.
- you may have to repeat the above a few times... A ford mechanic once told me it takes like half a day to properly "burp" the system w/ all the time needed to let the car cool down.