Prepare the chicken: season thighs with salt and pepper and coat with 1 cup BBQ sauce; either cook in a crockpot on low for 4 hours, shred, return to sauce and cook 30 more minutes, or bake at 425°F for 20–25 minutes until cooked through, then shred and toss with remaining sauce.
Preheat the oven to 350°F for finishing the squash boats.
Trim the ends of the spaghetti squash, cut it in half lengthwise, and scoop out the seeds.
Place squash halves cut-side up in a microwave-safe dish and microwave 12–15 minutes, or until the flesh easily shreds with a fork; set the shells aside for stuffing and use a fork to shred the flesh into noodle-like strands.
Heat 1 tablespoon olive oil in a large skillet over medium heat, add a pinch of red pepper flakes and the minced garlic, and cook 30 seconds until fragrant.
Add the diced red onion to the skillet, season with salt and pepper, and cook about 5 minutes until beginning to soften.
Add the shredded spaghetti squash, 1 cup shredded BBQ chicken, and 1/2 cup BBQ sauce to the skillet; mix until combined and adjust salt and pepper to taste.
Place the empty squash shells in a baking dish and evenly divide the BBQ spaghetti squash mixture between them.
Top each filled squash with shredded mozzarella and smoked gouda, add a few small dollops of extra BBQ sauce if desired, and arrange reserved onion rings on top.
Bake at 350°F for 10 minutes until cheese is melted and bubbly, then broil 1–2 minutes if you want the cheese browned—watch closely to avoid burning.
Garnish with chopped cilantro and a sprinkle of red pepper flakes; serve (one spaghetti squash boat equals two servings).
