You should do it when the tank is empty. The other link I gave you gives specific directions on how to place plants, and the gravel around them. Read through it again (the one on "How to set up a Planted Tank") and it gives a detailed step by step guide to how to do it.
I didn't wait any time from filling the tank with water and putting fish in. I rinsed the gravel very well, until the water ran clear from it. I didn't let it dry, you are just gonna fill the tank with water anyway. I used a small plate (saucer) to splash the water on to prevent the stream of water from disturbing the substrate.