Arrange a rack in center of oven; preheat to 350°. In a large skillet over medium heat, heat oil. Add onion; season with salt. Cook, stirring occasionally, until softened, about 7 minutes. Add ground beef and cook, stirring, until browned, about 7 minutes. Drain fat, if desired.
Add garlic, tomatoes, water, sour cream, chili powder, cumin, and cayenne and stir until combined. Cook, stirring, until slightly thickened, about 5 minutes. Stir in cilantro.
In a 13” x 9” baking dish, spread tortilla chips in an even layer. Top with half of ground beef mixture, half of cheddar, and half of pepper Jack. Repeat for a second layer. Top with more cilantro.
Bake taco bake until cheese is melted and tortilla chips are softened, about 20 minutes. Let cool 5 minutes before slicing.