As others have said, you only use the grates you need in whatever combo - example drip pan on the lower grate, food on the main grate. You will need to use the main grate to support the upper grate, when you use it in that configuration. Another tip, the upper grate is also your "searing grate" - flip it over with the long handles/legs pointing up and set it on top of the charcoal basket handles.
I usually only do long heat soaks for pizza/bread on the stone. Sometimes for whole chicken on the upper grate, if I'm doing it indirect. Even for low/slow cooks, I'll just let the KK come up to near target temp, with grates in place. Then add the food.
dstr8 - you beat me to the punch. I was looking for a recipe, as I recognized what you were doing on the KK as very similar. It's also similar to what Emeril does.
http://www.foodnetwork.com/recipes/emeril-lagasse/perfect-roast-chicken-recipe.html