Usually most of us use the vacuuming of the substrate or bottom of the tank as an opportunity to change the water, so we add new, and dechlorinated, water back to the tank. I am a heavy water changer and replace 50 to 70 percent of my water every 1 to 2 weeks. For me I put the de-chlorinator directly into the remaining water of the tank and put the temperature adjusted water from the tap directly into the aquarium, this method usually requires more de-chlorination, for example I put 70 gallons worth of water treatment into the aquarium before filling the missing 40 gallons (my main tank is 75 gallons). Alternatively you can pre-mix your water in buckets or other containers then place that water into the tank. When using this method you treat the volume of the container not the tank.
To summarize, you treat the whole tank volume when filling directly from the tap. When using containers you only treat only the volume of the container. There is some debate which method is best but for me I have been adding the water to the tank for years.
When the water is treated with chlorine only you can age the water for a while before using it, de-gasses the chlorine out, but if your water is treated with chloramine, you cannot age the disinfectant out of the water, and you must use some form of water treatment. I don't use this method because storing 40 gallons of water is problematic.