If you add the Prime before you fill with the hose the chlorine/chloramine will be neutralized nearly instantly. This means there is no reason to turn off filters. Many people do water changes of 25% without any water treatment, post #19
here explains a bit about that.
Most of my tanks are drilled with overflows for water changes, hang a hose on the tank & time it out a 4 gpm. I add dechlor after it is done draining, without turning off filters, and don't have any problems. The amount of disinfectant added to tap water is enough to prevent any bacteria in a sealed, pressurized supply system with the occasional intrusion from outside the system due to a bit of leakage.
An aquarium has an amazing amount of bacteria compared to a water supply system. The disinfectants in tap water will kill a small percentage of that bacteria, but in the process will be depleted doing just that. If anyone has any experience with swimming pools you know that you have to continually add chlorine, not just at the start, as it does get used up due to the bacterial level, as well as some gassing off. I'm far from being a chemist, I'm sure someone will come along and explain in more technical terms what, and how this works.
Prime contains ethylenediaminetetraacetic acid, or EDTA, which binds any metals through chelation. This means any copper, lead or so on is not an issue when this product is used. This is also why a product such as this is suggested when using a private well for a water supply, while there are no disinfectants present, there is a good chance of having metals in the water due to agricultural use of fertilizers and pesticides.