Topping up fluid

While I'm looking at cooling fluids (see other thread about cool heater) whats the best method of topping up water. Did check the radiator last weekend and added a small amount to top it up, looked at the expansion bottle (the plastic one with min and max on it) and that was (when cold) down at the min mark. Should I top that up as well? Sure I read a label somewhere that says dont do that yet just seen in the service manual it says top it up there when you do a fluid change? Confused?