As 4 jaw states above, that method will give you the TOTAL CC's of the cylinder, but will also include any positive or negative piston dome CC chamber displacement.
If you have a domed piston or a dished piston, you will not get a correct "head chamber" CC reading.
Since the heads are off the engine, you're amost home free. Invert them, place them perfectly level on a bench and CC the chambers that way. Then you will be able to accurately choose the correct parts for your engine.
Here is some good info on CC'ing your heads, and a cheap kit to do it with.