What is wrong with just sucking as much gravel as you feel comfortable
using a big size hose? The only think that I'd be worried is
releasing gases from the substrate into the water. So it makes sense
to remove gravel during a water change.

Putting the new gravel can be done with a big size funnel. That way
it will not freely fall tru the body of water, but it will end up
being released on the bottom. Make sure the tube of the funnel is big
enough to not cause cluttering of the gravel. It requires small
potions of gravel being poured tru the funnel, but that is exactly
what you want anyway.

If you want to use Fluorite you need to clean it very well. Fluorite
is not that hard to rinse to a level where it produces just a slight
hazing of the water. Browse to find out how to rinse it if you want
to use it.

-Nikolay