Make the chicken: Season chicken thighs with salt and pepper and coat with 1 cup BBQ sauce. Either place in a crockpot and cook on low for 4 hours, then shred and return to sauce, or bake at 425°F for 20–25 minutes until cooked through, then shred and toss with sauce.
Prepare the squash: Cut off the ends of the spaghetti squash and halve lengthwise; scoop out the seeds.
Cook the squash flesh: Place squash cut-side up in a microwave-safe dish and microwave 12–15 minutes until the flesh shreds easily with a fork. (Alternatively roast in the oven until tender.) Use a fork to scrape the flesh into noodle-like strands, keeping the shells intact for stuffing.
Preheat the oven to 350°F.
Sauté aromatics: Heat 1 tablespoon olive oil in a large skillet over medium heat. Add a pinch of red pepper flakes and the minced garlic; cook about 30 seconds until fragrant. Add the diced onion, season with salt and pepper, and cook about 5 minutes until softened.
Combine filling: Add the shredded spaghetti squash flesh, 1 cup (or 1/2 cup depending on mixture instructions—use 1/2 cup here per ingredient list) of BBQ sauce, and the shredded BBQ chicken to the skillet; stir until evenly combined and taste to adjust salt and pepper.
Assemble boats: Place the empty squash shells in a large baking dish and divide the BBQ spaghetti squash and chicken mixture evenly between them. Sprinkle evenly with shredded mozzarella and smoked gouda. Dot a few small spoonfuls of extra BBQ sauce on top and arrange reserved onion rings if using.
Bake: Bake at 350°F for about 10 minutes, until cheese is melted and bubbly. For browned cheese, broil 1–2 minutes watching carefully.
Finish and serve: Garnish with chopped cilantro and red pepper flakes. One spaghetti squash boat equals two servings.