Two chucks, one smoker (WSM)

Just being in the same smoker won't cause any flavor cross over.

If you put them in a pan while they are still smoking, you won't get the smoke penertration you would if you just set them on the grills. They should still be tender and good, but they will be better if smoked out of the pan, and on the rack.

If the Chucks are big enough that you need to use both top and bottom, and the top juices will drip on the bottom, think about cooking them standing on their side using a rib rack.