The method that I find worked well for me, was put all the soil and everything in, then put the plants in, and add water. Or fill about 1" past the substrate. The problem is, when you plant everything, the substrate gets stirred up quite a bit. That's why it's easier to plant first on most cases.
When you add the water, hold your hand in the tank and pour the water slowly onto your hand, so it spreads evenly and doesn't penetrate into the substrate, causing major cloudiness. But you probably knew that one already!