I just made a batch to go into the smoker tomorrow. Kind of a pain in the butt. I made a dozen by splitting them up the middle, scooping the seeds, filling with the cream cheese mixture and laying a half strip of bacon on top and six by cutting off the top, scooping, filling, sticking a bit of bacon in the top, wrapping with a half slice and skewering with a toothpick. The halving method is 150% easier. I took a couple of cheap foil disposable steam table pans that will just fit into the smoker, put the halved jobs in one and turned the other upside down, poked some holes in it and stood the capped peppers upright by tucking them in the holes. I'll put that on the next shelf up.
The filling I used was about 8oz softened cream cheese, four scallions minced, and about 3 heaping tablespoons of my regular dry rub mix - 4 parts brown sugar, 2 parts chili powder, 1 part smoked paprika, 1 part cumin, 1 part salt, 1 part black pepper, 1 part granulated garlic.
I might sprinkle a little more rub over the top of the whole shebang before I put it in the smoker. Only thing I'm concerned about is that the bacon I used is the extra thick dry cure and it might not cook fully before the pepper starts to disintegrate. I got big honking jalapenos just to be sure they stand up. Most of them are a good 3.5-4" long.