Lay down eggcrate along the bottom of your tank first. This will elevate your rocks and spread out the weight along the bottom of the tank rather than creating pressure points on the tempered bottom.
Then just fill in the substrate over the eggcrate and around the rocks.
Back to the original question though... What is the ideal flow for a Malawi system? I'm setting up a 90 mbuna tank and am wondering the same thing.
Is there a reccomended turnover?