Heat oil in a large skillet over medium-high heat. Transfer about 3/4 cup of the onions to a blender; set aside to use later. Add remaining onions, garlic, 1 of the jalapeños, 1 teaspoon of the cumin and salt and cook, stirring often, until softened and golden brown, 8 to 10 minutes.

Transfer about 1/2 cup of the bell peppers to blender with reserved onions, then add remaining to skillet and cook, stirring occasionally, until tender, about 10 minutes. Remove skillet from the heat and stir in cream cheese, 1 1/2 cups of the cheddar cheese and cottage cheese. Add salt and set filling aside.

Meanwhile, add tomatoes, remaining jalapeño and remaining 1 teaspoon cumin to blender with reserved onions and bell peppers and process until smooth. Transfer to a medium pot, bring to a boil over medium-high heat, then reduce heat to medium and boil gently, uncovered, until thickened, about 20 minutes. Season with salt and set enchilada sauce aside.

Preheat oven to 350ºF. Spray a 9- x 13- baking pan with cooking spray then spread about 1/2 cup of the enchilada sauce over the bottom of the pan; set aside.

Heat a large skillet over medium heat. Working with one tortilla at a time, warm it in the skillet, flipping once, until soft and pliable, about 30 seconds. Transfer tortilla to a flat surface and arrange about 1/3 cup of the filling down the center. Roll up tortilla snugly and place in baking pan. Repeat process with remaining tortillas and filling. Pour remaining enchilada sauce over the top
and sprinkle with remaining 1/4 cup cheddar cheese. Bake until bubbly and hot throughout, about 25 minutes.