Preheat oven to 375 degrees. Grease a 9x9" baking dish for the casserole. Use a different pan for baking the squash.
With sharp knife slice top out of squash. Stand squash flat on the cut side. Slice squash in half. NOTE: this squash was not easy to cut, pretty tough skin.
Scoop out the seed and membrane.
Brush inside of each half with oil; sprinkle with salt an pepper. Place cut sides down in baking pan.
Bake for about 40 minutes or until squash is fork tender.
Remove from oven; let cool for about 10 minutes or until cool enough to handle.
REDUCE oven heat to 350 degrees.
Using a fork, scrape out the spaghetti squash. Place in bottom of prepared baking dish. Sprinkle with salt and pepper and a small amount of the taco seasoning; toss. Spread squash evenly over bottom of baking dish.
In large skillet over medium heat, cook meat, onion, pepper, and garlic until meat is cooked. Add taco seasoning and add salt and pepper to taste. Add pepper flakes for a little more heat. Stir in refried beans and black beans. Remove from heat.
Layer beef mixture over squash.
Drain some of the liquid from Rotel tomatoes. Spread tomatoes evenly over top of meat layer using about 2 tbsp. of the liquid.
Bake for 40 minutes or until bubbly. Remove from oven; sprinkle cheese evenly over top. Return to oven and bake a few more minutes until cheese has melted.