Doing my first brisket this weekend...

I usually try to put the butts above the brisket...self-basting!

I cook fat cap down to preserve the bark on the brisket flat...also, since the fat cap is "throw away" it can help to buffer the meat from the heat coming from below.

You can make great brisket either way.

I cook butts to about 200-205 and then put them up (I use blankets, but that's a different story) for about 3-4 hours - they'll, obviously, hold for longer than that. The holding time definately makes a difference...and you can "overcook" the butts by holding them too long...however, it'll still taste good.

I always go with the fat side up for the self basting effect. If you put the butts above the brisket, I guess you should be OK, and you get the protection from the fire below like chad says. You could also consider layering some strips of bacon on top of the flat to help keep things basted.

Are you going to mop the butts and/or the brisket? This could also affect your plans for how to arrange the meats.

Good luck!

Yep, with butts to go in there too I'd do this one fat cap down, with the butts above. Shouldn't go wrong.