I think you will be OK smoking on separate racks. I would suggest probing the bottom meat to begin, and remove when you hit the desired IT. Then, I would move the probe to the other half of the meat to monitor IT of that piece. I would not be surprised if they both reach temp at about the same time, assuming they are each 9# or so.
I think Tony's 9# roast took about 5 hours, so you better get the 9# boys on the smoker soon!