You don't. When the vent door is open or the Temp control cable is closed air does not flow through the heater core so the hot heater core only radiates the heat inside the heater box. This heat is not as bad as it sounds because the fan is not blowing heated air inside the car. On an AC car...the AC needs all the help it can get. That is why the AC cars have a shutoff valve AND tinted windows...and more fan blades along with a fan shroud to pull (more) air through the condenser.
I mainly wanted to install the heater box back in for the blower fan, and to defrost my windows. My car gets real hot during the summer and the fan seems to help out a bit. So once I turn on the blower fan with the heater core connected will it blow hot air? And do I need to drain my cooling system to install the heater core?
Yes it will blow hot air when the fan is on. Drain the radiator and remove the heater hoses from under the hood. Leave the hoses connected to the heater core. This way you won't get the carpet wet. Sit the heater box on the floor before pulling the hose out of the firewall. Be sure to keep the hoses up high once they come out of the firewall the lower the hose outside of the car and drain the hose out on the driveway/ground/yard/shoes.
The new heater core is already installed in the heater box. I got the hoses clamped down at the heater core and running trough the firewall. I just need to connect both hoses everything else is done, that's why I am asking if I should drain the cooling system so I dont have coolant bursting out when I disconnect the bypass hose.
Shouldn't be an issue, both connections are on top of the core. Usually if it needs to flow a given direction they use different size hoses.
Val- I gave you the wrong info. After digging through a bunch of pics I see the bottom hose goes to the water pump. Here's a pic of a low mileage Maverick I got from eBay, other pics from shop manuals and one from a auto repair book.
Crossing heater hose connection is a old shade tree trick to improve heat output... Generally it helped as the flow cut a new path thought the sediment but real cause was dirty cooling system... I've never seen a properly operating std system(no A/C) that reversing hose connection made a noticeable difference...