When applying your BBQ rub to the brisket, don't worry about getting it on the fat. Aim for the exposed meat since it absorbs the flavor.
When applying rub to the brisket, do it on a large sheet of heavy duty aluminum foil (the 20 inch side stuff is the best). This simplifies the process by allowing you to wrap it up with all the rub inside and storing it in the refrigerator. The moisture from the brisket is going to turn the rub into a paste that will help it stick to the meat and help it absorb the flavors.