There's also a tool that you hook up to the radiator filler neck, it screws on (just like a rad cap would), then you have a valve turned a certain way, hooked up to an air compressor. This sucks all the air out of the system (you have to drain the car first btw...), making it a complete vacuum in your coolant system. On the other side of all this is a bucket full of the coolant you're planning to put in the car, and a hose attached to said valve in the bucket. Once you turn the valve, it sucks all the coolant into the system, no air at all.
Trouble is, I forget what this particular device is called. All I know is my buddy Wes helped me flush out and fill my Mk2 back in the day when we were trying to trace down an overheating issue (turned out to be a bad radiator). Worked absolutely great, hopefully someone on here knows WTF I'm on about and can give us a name of this tool.
Oh, and if you have a heater core but haven't hooked it up, you're possibly hearing coolant that got stuck in it sloshing around while you drive.