Make the BBQ chicken (slow cooker method): Season chicken thighs with salt and pepper, place in a slow cooker with 1 cup BBQ sauce, and cook on low for 4 hours. Remove and shred with two forks, then return to the cooker and stir in sauce; cook 30 more minutes. Alternatively, bake at 425°F: season thighs, coat with BBQ sauce, and bake 20–25 minutes until cooked through, then shred and toss with sauce.
Prepare the squash: Cut the ends off the spaghetti squash, slice it in half lengthwise, and scoop out the seeds. Place cut-side up in a microwave-safe dish and microwave 12–15 minutes, or until the flesh shreds easily with a fork. Reserve the shells for stuffing.
Heat a large skillet over medium and add the olive oil. Add a pinch of red pepper flakes and the minced garlic; sauté about 30 seconds until fragrant. Add the diced onion, season with salt and pepper, and cook about 5 minutes until softened.
Add the shredded spaghetti squash and 1/2 cup BBQ sauce to the skillet with the onion and garlic. Stir in the shredded BBQ chicken and mix until everything is well combined. Taste and adjust salt and pepper as needed.
Assemble the boats: Place the empty spaghetti squash shells in a baking dish and divide the BBQ spaghetti squash and chicken mixture evenly between the halves. Top each with shredded mozzarella and smoked gouda, dot with a few small spoonfuls of extra BBQ sauce if desired, and arrange reserved onion rings on top.
Bake at 350°F for about 10 minutes, until the cheese is melted and bubbly. If you want browned cheese, place under the broiler 1–2 minutes, watching closely.
Garnish with chopped cilantro and a sprinkle of red pepper flakes. Note: one spaghetti squash boat counts as two servings.