In a large pan melt the vegan butter over low heat. Once melted add the sliced onions, sugar, and salt. Cover with a lid and cook for 10 minutes, do not stir. After 10 minutes remove the lid and stir, the onions should be cooked down and getting softer. Place lid back on and cook for another 10 minutes. Remove the lid and then mix again continue to cook uncovered for 30 minutes over low heat and mix occasionally.
After 20 minutes of cooking the onions preheat oven to 400°F (204°C).
In a medium pot bring salted water to a boil. Cook pasta to preferred doneness, strain when done.
Meanwhile, in a medium pot add the cheese sauce ingredients, save about ¼ of the vegan mozzarella and vegan parmesan to sprinkle later. Cook over medium low heat whisking frequently until everything is melted down and uniform.
Once the onions, pasta, and cheese sauce are all done add the Better than Bouillon to the water and mix to make broth. Pour over croutons and allow it to soak in. *this can be done with vegetable broth as well.
Pour the cheese sauce over the pasta, reserving a bit to pour on top of mac and cheese later. Mix to coat the pasta. Add in most of the cooked onions but reserve some for the top as well.
Add half of the pasta to the baking dish. Then add the reserved vegan mozzarella, vegan parmesan, and about a ¼ of the breadcrumbs. You want to save most of the croutons for on top.
Add the remaining pasta. Then top with remaining cheese sauce, onions, and croutons.
Bake in oven for 12-15 minutes or until crispy on top.
Let it rest for 5 minutes and then serve. Garnish with fresh thyme or oregano if desired.