I've done it both ways - separate then cook for a few hours, then cube, sauce, etc. I've also done it where I rest the whole brisket together and make burnt ends right before turn-in. IMO, it depends on how you trim your brisket to begin with. If you trim agressively and throw the point on for another couple hours, you'll overcook them.
I don't consider what I turn in to be a true burnt end, but rather a cube of brisket.
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