I add only the amount of conditioner needed to condition the water you're adding back. For a 25% change, add only enough conditioner for the 25% you're adding back.
Some people dose the entire tank. I view it as a waste, however, if you're using a product like stress-coat, it may not be a bad idea because this supposedly adds a protective slime coat to the fish. But if your tank is healthy it probably isn't necessary. You can't go wrong either way but it is more expensive to dose the entire tank.