When I changed over my scape and substrate, I:
1 - disconnected the filter
2 - Rinsed all the media in the filter water
3 - Poured the lot into the tank and let the water settle
4 - made sure the mulm (now at the bottom of the 1 cm of water) was evenly spread.
5 - Layered a ½cm layer of Leonardite on top (which also soaked up the water)
6 - Put my Tropica Substrate on top
7 - Layered the surface with 2 inches of playsand.
Job done (This is all on the first page of my 'Under the forest canopy' journal)
Andy