Preheat the oven to 375 degrees F.
Spread the chips on a large flat pan or Dutch oven and place in the oven for about 15 minutes while prepping ingredients.
Crumble the beef in a large cast iron skillet over medium heat. Cook for about 3 minutes or it begins to brown, stirring occasionally. Stir in half of the chopped onion. Cook until browned, stirring occasionally.
Mix in the Mesquite seasoning (or seasoning of your choice), oregano, cumin, chili powder and smoked paprika. Cook over low heat for 4 to 5 minutes, to allow flavors to combine.
Stir the black beans and pinto beans into the meat mixture. Stir in the garlic cloves and let simmer over low heat for about 5 minutes.
In a medium bowl combine the sour cream, pickled jalapenos, 2 teaspoons red pepper flakes and honey. Add a little of the jalapeno juice until it reaches a pourable sauce consistency. Set aside.
In a separate bowl, combine the cheddar and Monterey jack cheese and set aside.
Add the Velveeta cheese to a small saucepan over low heat. Stir in the butter and heavy cream until blended. Cook for about 4 to 5 minutes stirring occasionally until the mixture is smooth. Stir in the liquid smoke and 1 teaspoon red pepper flakes. Cook on low heat for about 2 more minutes, stirring occasionally.
Remove the chips from the oven and place on a serving dish. Sprinkle about ⅓ of the shredded cheese on the top, followed by ⅓ of the meat mixture, ⅓ of the cheese sauce and a generous drizzle of the sour cream mixture. Repeat until the ingredients have all been used.
Top with the remaining half onion and jalapenos. Serve immediately.