What's the best way to treat soup?

Let’s say you have a huge pot of soup that you would like to enjoy throughout the week – or at least for a few days. What would be the best method for reheating the soup that would allow for the freshest – and least spoilage?
My assumption here is that you take the portion you would like to consume and heat it thoroughly. However, I have had a few people tell me that heating the entire pot of soup is fine – and preferable – every time, and then just put it back in the fridge. This seems to be encouraging bacteria growth, by constantly bringing it up to a temperature that will take a long time to cool. But the people who have argued for this method seem to think that if you get a nice boil going, you’re killing any of the bacteria that had grown since the last boil.
Anyway, I’m really interested in the science here. Does anyone know?