Deck height

You need to know your swept volume to calculate compression.

You can just use the book values, or measure it. Measuring it will be most accurate. Book values will be close enough for swept volume calculations, but you need to measure the information to figure out clearance volume.

If you mean measuring the volume above the piston, yes, I recommend using the method that I have in my how to link. You don't know where it was from the factory, or if anybody has machined it since. The only way to know what you have is to measure it.

you can either use water, or just measure the bore and piston to deck height and move on.