Stewart--
Check the "Dimensions" of the Shoulders and make sure there is plenty of room on one grate. The top grate has a bit higher temperature, assuming you may have added the "Clay Plate" at put on top of your water pan. I NEVER put water in my pan, but I do wrap it in foil, along with the 14 inch clay plate, which can be bought at most Home Depot's for under $10.00. Just set it on the top of the water pan, make sure both are wrapped in heavy duty foil and start smoking. 
Please keep in mind, both briskets and pork butts or shoulders vary, and depending on what time you want to eat, plan ahead accordingly. You may be looking at 10+ hours or more to get them to 170, and if you desire, take them off, wrap them in foil, put them back on and smoke them up to about 210 for tenderness. It's VERY HARD to mess up a pork butt or shoulder because of the fat contained within. Let them "Rest" for an hour or two, then pull the pork. I'd wrap them in towels and put them in a cooler during the resting period. It will be PLENTY hot when you pull the pork.
I have a DigiQ Guru 2 DX and I leave ALL my vents closed except the top one, and I only open it about 1/4 to 1/2 open, and set my pit temp at about 225. You can cook them at higher temp, and there will be a hundred posts after mine telling you what's worked for them.
You have a GREAT Smoker.
Good Luck.