You really want to fill the cooling system from the bottom to force the air out the top. This is normally what happens when you fill the system through the radiator cap, the coolant flows down through the radiator, through the lower radiator hoses to the engine and fills the engine from the bottom up. There should be a way for the air to escape the engine at the thermostats and up the upper hoses to the top tank of the radiator.
Regardless of how you try to fill it, the water is going to go down and the air is going to try to rise and may collect somewhere that is not beneficial to cooling.