From reading the recipe, it looks like the salt/sugar mixture you put on the outside of the roast is a dry brine. This is designed to help make the meat more flavorful and to help it retain moisture during the long cooking process. Certainly you can salt in the morning and stick it into the smoker, but the longer you let it sit with the dry brine, the more the salt mix will penetrate the muscle tissue and have a better effect. These big roasts get dried out pretty easily, especially if you don't have a huge fat cap on the top of the shoulder.
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