You can go either way but it doesn't hurt anything leaving them in, and if you get the plates with the dimple in them you don't even need to remove the screw on top. With the dimple plates its as easy as removing the stock cover and bolt on the new plate and your done.
I purchased the plates and removed the valves, used a hole saw and removed the end plates of my pipes and pulled out the baffles. Installed a stage 2 carb kit and a K&N air filter. This is how it sounds. I can get it to pop on decel when I want to. It has to be just the right conditions. http://www.youtube.com/watch?v=yI-7vlcyZrU