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Heat your smoker to 300 degrees F.
Slice the jalapeno peppers in half lengthwise and scoop out the insides with a spoon.
Add the cream cheese (+ cheddar cheese, if using), smoked paprika, garlic powder, salt and pepper, and red chili flakes to a bowl and mix well.
Fill each jalapeno pepper half with the spicy cheese mixture. You might have some leftover, depending on the size of your peppers. Just distribute evenly.
Wrap each stuffed jalapeno boat with a slice of bacon. Pierce with toothpicks to hold the bacon in place. NOTE: You can use half a bacon slice with smaller peppers, and as a calorie saver.
Sprinkle the poppers with extra smoked paprika and red pepper flakes and smoke them for 60-80 minutes, or until the peppers soften and the bacon is starting to crisp. You can blast them with the broiler a couple of minutes at the end if you need to.
Remove from heat, cool slightly, and serve.