Preheat oven to 400°.
Line a rimmed baking sheet with parchment paper.
Mix brown sugar with garlic, smoked paprika, salt, pepper, dry mustard and red pepper flakes together on a plate.
Dredge bacon in brown sugar mixture on both sides and layer on lined baking sheet.
Bake for 12 minutes. Remove from oven and set aside to cool. When cooled, cut into bite sized pieces.
Lower oven temperature to 325°.
Meanwhile, cook onion and bell pepper in olive oil over medium heat until vegetables are softened, about 6- 8 minutes.
Using a 3 to 4 quart baking dish, add pork and beans, cooked vegetables, homemade barbecue sauce, liquid smoke and chopped bacon. Stir to combine.
Cover with a lid or foil and bake for 2 hours. Remove lid or foil and stir beans.
Continue to cook 30 minutes to 1 hour until beans are thickened.
Remove from oven and allow to rest 10 minutes before serving.