The common way as far as i know if to have the refrigerant evacuated of the system first. I do not suggest continuing working on a charged system while under the dash unless you have instructions they you feel very sure of. Because one it is a large fine to knowingly release refrigerant into the atmosphere, and two refrgerant like to raise and wents poorly, if your laying under the dash and the refrigerant starts to leak it will collect and be trapped in the the high points of the dash, the car, and the garge roof.
Any good A/C shop should be able to evacuate the refrigerant and disable the compressor while you R&R the heater core. Then refill it with fresh refrigerant and oil.