What I do when filling up the engine with coolant/water is:
Assuming engine cold:
(1) Turn the heater to "on" so that coolant will fill/circulate through the heater core
(2) Take out the temp sending unit from the manifold. Fill up with coolant until it's about to come out of the temp sending unit hole. Replace the temp sending unit.
(3) Fill with coolant the rest of the way until it just covers the radiator fins
(4) Start the engine and let it start to warm to operating temp
(5) Add coolant as needed. When the thermostat opens the level usually drops (having a IR temp gun to check the temp of the radiator hose is useful in gauging just when this is occurring)
(6) When you don't see any more bubbles in coolant in the radiator, you're done. Radiator cap on. Engine off.
(7) Later, after the car has cooled down, check the level. Coolant should just cover the radiator fins. Not any higher.
+1 on putting a small "breather" hole in the thermostat. Helps "burp" the system. Some thermostats already have them.
What I've always done is to remove the heater hose (where it plugs into intake manifold) and fill SLOWELY until I get water up to the fitting. Then when it's there plug the hose back in. If you do not have a spring in the lower radiator hose you can hand pump that to try to get the air "up". Just what I do. Mel