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I'd say leave it out, but that's based on the way I smoke BB. I do 20+ hr cold smokes and don't let the temperature get over 100. Others here do a little higher and smoke to a specific internal temperature
I think it's half and half for methods, but even then I'm not sure about water come to think of it. Hmm....
Leave it out. You want to dry the sides before putting smoke to them. If you leave the pan in, the meat will never get dry. Also low and slow is the way to go for bacon sides.
I smoked mine along with ribs last time around 4-5 hours at 225 with a water pan and we loved it. Everyone has their own way to do it. Its all about how you like it.
I would take it out for the dry time...usually a hour or so at a 100 degrees or so. then when you are putting a heavy smoke to them you can put the water back in to get the temps to 152 or what ever temp you are shooting for a little faster then with out water.