This is an ongoing debate, and I don’t expect this will end it. At Saddleback we always cook our brisket fat side up.
This does a couple things. First from a practical stand point, when you cook a brisket fat side down it has a tendency to stick to the grates of your smoker, making it difficult to move.
Second, because the fat sticks to the grates it will ensure you will lose some of your hardly fought for bark.
BUT - we use an offset smoker, the smoke from our wood needs to travel a long distance before hitting our brisket. This is a very indirect feat source. If you use a cooking method that has a more direct flame on the meat you may want to consider going fat side down. The thick layer of fat will help protect the meat from the heat.
As always with BBQ experimentation is always the best part because at the end of the day you get to eat some really great food.
We’d love to hear which method you prefer and why!