From the wording of your post, it sounds like you already have the substrate in the tank.
If so, my suggestion is that every time you do a water change, you gravel vac. (lightly) as much area of the substrate as possible to remove excess sediment from the surface.
Over time the sediment that is left will work it's way down into the substrate and eventually to the very bottom, but for now a few light gravel vacs. should do the job for you.
I am not a great believer in heavy washing of Flourite. I like to keep as much of the extra 'stuff' as possible. After all it's an expensive substrate.
I just rinse it once to get the 'coffee slug' out of it and throw it in. So I know what you're experiencing now. It will settle down over time.
Len