Prepare the Squash Boats: Trim the ends from the squash and slice each one in half lengthwise. Use a spoon or melon baller to scoop out the seeds and flesh, leaving a ¼-inch thick shell. Finely chop the scooped-out squash flesh and set it aside.
Pre-cook the Squash: Arrange the squash shells cut-side down in a large skillet.
Add ½ inch of water, cover, and steam over medium heat until just tender, about 5-7 minutes. You may need to do this in batches. Carefully transfer the steamed shells to a buttered baking dish, cut-side up. Dot the insides with butter and season with salt and pepper.
Sauté the Aromatics: Wipe the skillet dry and add the olive oil, heating it over medium heat.
Add the diced onions and sauté until softened, about 5 minutes.
Stir in the ground cumin, oregano, and minced jalapeño, and cook for another minute until fragrant.
Add the reserved chopped squash flesh and continue to cook, stirring occasionally, for 5 more minutes.
Create the Filling: Stir the cooked kidney beans and green chiles into the skillet.
Season with salt and pepper to taste and cook until heated through.
Remove the skillet from the heat and let the mixture cool for about 10 minutes.
Once slightly cooled, stir in the sour cream and cubed Monterey Jack cheese.
Assemble the Boats: Preheat your oven to 350°F / 175°C. Generously spoon the bean and cheese filling into each squash shell, mounding it slightly. (Make-Ahead Note: At this point, you can cover and refrigerate the stuffed squash for up to 48 hours. Just let them sit at room temperature for 30 minutes before baking.)
Bake and Garnish: Bake for 20 to 30 minutes, or until the filling is hot, bubbly, and the cheese is melted.
Garnish with fresh minced parsley or cilantro before serving.