In a large bowl, thoroughly combine ground beef, pork sausage, shredded cheese, diced jalapeños, and 2 tablespoons of the BBQ dry rub.
Carefully stuff each dry manicotti shell with the meat mixture, ensuring the filling is packed tightly from end to end with no air pockets.
Wrap each stuffed shell tightly with bacon, using approximately 1.5 to 2 slices per shell, ensuring the pasta is completely covered to facilitate even softening.
Season the exterior of the bacon-wrapped shells with the remaining 1 tablespoon of BBQ dry rub.
Place the shells in a sealed container and refrigerate for a minimum of 4 hours, or overnight, to allow the moisture from the meat to soften the pasta shells.
Preheat your smoker to 250°F (121°C) using a hardwood like hickory or oak.
Place the shotgun shells directly on the smoker grates and smoke for approximately 90 minutes.
Increase the smoker temperature to 300°F (149°C) and brush the shells generously with BBQ sauce.
Continue cooking for another 20 to 30 minutes until the bacon is crisp and the internal temperature of the meat reaches 165°F (74°C).
Remove from the smoker and allow the shells to rest for 10 minutes before serving.