Preheat oven to 300 degrees.
Heat a large skillet over medium-high heat.
Add in the sliced bacon. Cook until bacon begins to render fat and then stir in chopped onion. Saute bacon and onions together until onions begin to soften and bacon is browned and slightly crisp. This should take about 5-6 minutes. Drain off excess fat off bacon.
Mix together tomato sauce, brown sugar, molasses, maple syrup, dried mustard, vinegar,apple juice, water, and salt together. Add in bacon and onion mixture and cooked beans and gently stir to combine.
Pour bean mixture into 2 quart oven safe dish. Beans should be pretty well submerged in liquid and mixture should be relatively loose. If there does not seem to be enough liquid in baking dish, add up to 1/2 cup additional water or juice. Cover pan with foil or oven safe lid.
Bake covered for 2 hours. Uncover and bake for another 30-40 minutes, until thickened.