Sure, the header tank is always full, it doesn't matter how you install it, as long as the clunk can move in it freely. If you run the main down all the way and get into the header fuel, you just have to make sure you don't get it low enough to start sucking air. there should be no air in the header when you are flying to suck bubbles. Thats the purpose of a header tank.

AS stated above, the clunk should sit more toward the middle, but I still have mine back quite a ways, not exactly in the center. I like to get most of the fuel out when I de-fuel.