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I just finished a q class from one of the best cooks in the nation. I was surprised he didn't separate the two before cooking. Who separates and who doesn't?
I do it both ways. Sometimes I separate them, & sometimes I don't. Can't really tell much difference either way. I usually leave enough fat on the flat to keep it moist if I separate them. I also smoke them in a pan, sitting in their own juices. If I don't separate them, I take as much of the fat out that is between the two that I can, then put my rub in between & put them back together. I also take the trimmed fat & put it on a rack above so it drips on the brisket throughout the smoke.