Anytime I'm using the top shelf I'm carefully aware about what's underneath it on the main space. I tried smoking 4 pork butts once, two on top and two on bottom, and gave up after 24 hours and just chopped them up. If I separate my brisket muscles I'm going into the cook knowing that the point on the top shelf is going to cook substantially slower than the flat on the main space. It's not a disaster any more - just an adjustment.