Doesn't really matter. On top, the melting fat won't penetrate the meat-- it can't. On the bottom, as is done with brisket, it might act as a shield against drying out the part of the meat closest to the heat. But, all in all, pork shoulder has so much intramuscular fat that it makes no material difference. Flip it over a couple times during the cook if you want, but it's not worth losing sleep.