I do that operation routinely, but I separate the manifolds first. Since it's difficult to get a solid mount on the assembled pair, and keep it from shifting around, I always mill them separately. Then, I snug both manifolds up to the head before tightening the bolts between them at the heat riser. I try to mill approximately the same amount of metal from each one, though. Doing both together is just a time-saver, it's not a better procedure.
Jerry