Put a large pot of water on to boil. Once it begins boiling add shells and cook according to the package directions.
While the water is heating, cook ground beef and onion over a medium flame until beef is browned.
Add taco seasoning, beans, and diced tomatoes. Be sure to add the juice from the diced tomatoes too. Simmer over low heat for for 5 minutes.
Remove from heat aside and let cool while the shells cook. Once the meat mixture is close to room temperature, add 2 cups of cheese and mix well.
In a small bowl, combine tomato sauce and salsa. Spoon 1/2 cup of tomato sauce mixture into each 13 x 9 baking dish.
Preheat oven to 350 degrees.
After the shells have been drained, spoon meat mixture into each shell and place it in a baking dish.
After all the shells have been filled. Spoon 1/2 cup of the tomato sauce mixture over the shells in each baking dish. Sprinkle 3/4 cup cheese over the stuffed shells in each baking dish.
Cover one baking dish with foil and bake at 350 degrees for 25 minutes. Remove foil and bake for another 5 minutes.