Fat up, fat down. The eternal argument. If I'm cooking in my off set it will be fat up. In the drum, or WSM even, I always go fat down. Gives the meat a little insulation from the heat coming from below. I assume you are doing a whole packer? Another trick to try would be laying a few slices of beef suet right on the flat part. Never tried it with brisket, but just did some venison and it came out great!
Going fat up when it is in the pan with the brazing liquid helps to tenderize the meat to a great degree.