If you are going to use a thermo the entire time, I would put it in the smaller one since that is most likely the first one to get done, then move it over to the larger piece.
I have a packer on now (whole brisket - flat + point). Took it out of the fridge, fired up the cooker, trimmed the brisket, and tossed it on the cooker @ 275*, It's been on since 8 am and I will check it in a few more hours. I will pull it once it probes like a hot knife through butter. Then I will separate the point from the flat, wrap the flat in foil, then in a towel, then into a warm dry cooler.
The point I will dice up, add more rub to, add some sauce, then back into the cooker for a while longer.
Have fun with your cook, enjoy your results.