I treat, heat & age the water before adding it to the aquaria, so I just treat that volume of water. Seachem says to treat the volume of the tank when adding directly from the tap, although some people apparently do fine treating for just the volume of the make up water... I don't really understand the rationale for treating for the entire tank volume if you're only changing part of the water, but I don't have to understand, either.
Somehow, I like the idea of making the water safe *before* there are fish in it...