Heat your oven to 350°F first so it's ready when you need it. Add the chopped bacon to a large skillet over medium heat and cook until it's crisp and deeply browned, which takes about 6 to 8 minutes. Use a slotted spoon to move the bacon to a paper-towel-lined plate, then pour off all but 2 tablespoons of the fat.
Return the skillet to medium heat with that reserved bacon fat still in the pan. Add the diced onion along with half the salt and half the pepper. Cook, stirring every so often, until the onion turns tender and starts to pick up some golden-brown color, about 6 to 8 minutes.
Add both cans of drained beans, the water, brown sugar, molasses, ketchup, mustard, vinegar, garlic powder, smoked paprika, and the remaining salt and pepper right into the skillet with the onions. Stir everything together well and bring the mixture up to a gentle simmer on the stovetop.
Pour the beans and all of that sauce into your baking dish, then scatter the reserved crispy bacon evenly over the top. Bake for about 45 minutes, until the sauce is bubbling at the edges and the beans have darkened slightly in color. Let the dish rest for 5 minutes before serving so the sauce can thicken up.