I make my own rub with salt, brown sugar, paprika, black pepper, garlic powder, chili powder, onion powder, and thyme. Apply it the night before.
As for smoking, I roll a hard smoke for 2-3 hours. You'll want to wrap it after the smoke period, so here's my thoughts on that. I'm not a hard-headed purist intent on burning a whole sack of charcoal, so I put my shoulder in a Pyrex dish and cover it with foil. I'll pop it in a 250° oven for the rest of the day. About 2 hours before serving, I'll uncover it, and put the Pyrex back in the smoker to finish. Pull it after an hour, and let it rest uncovered until you're ready to pull & serve. Total cooking time is 6-hours for a small Boston butt or over 12 hours for a bone-in shoulder. You want 25% of your cook time to be rolling smoke, 60-70% wrapped, and 5-10% of your time unwrapped to finish.
I use lump hardwood charcoal or Chef's Delight briquettes. For smoke, I'll use a combo of whatever hardwood chunks I have on hand: hickory, apple, pecan, and maple