Hey Jason. When you use the word substrate it refers to anything such as gravel, flourite etc....
Now that thats cleared up.... :hehe: I have succesfully added flourite to an already established tank. It was hard work and my tank was cloudy for a long time however it worked well. I didn't loose any fish and I am very happy I did it.
You don't have to bother taking that much water out or the fish. You can leave the fish in there and only take out as much water as needed so that your tank doesn't overflow when you add the new substrate.