Preheat oven to 300°F.
Heat a large skillet over medium-high heat.
Add in the chopped bacon and onion.
Cook until onions begin to soften and bacon is slightly crisp, about 6 minutes.
Drain off excess fat.In a medium bowl, mix together the tomato sauce, molasses, brown sugar, maple syrup, vinegar, mustard, salt, apple juice and water.
Stir in bacon and onion mixture and cooked beans.
Mix gently to combine.
Pour bean mixture into a 2-quart oven-safe dish.
Beans should be covered in the liquid mixture. If needed, a bit more water can be added.
Cover dish with foil or an oven-safe lid.
Bake covered for 2 hours. Uncover and bake for another 30-45 minutes, until thickened.
