Preheat oven to 375 degrees.
Cut squash in half and scoop out the seeds with a spoon. Season the spaghetti squash with a little bit of olive oil, salt and pepper.
Lay skin side down on a rimmed sheet pan that is lined with aluminum foil.
Cut your chicken breast so you have four pieces of chicken. Place the chicken on the sheet pan, season with salt and pepper.
Bake for 45 mins or until cooked to a touch with a fork. When the squash is cooked Scrape the flesh with a fork to create noodles and dice your chicken in to small pieces.
While the chicken and squash are cooking place the onions with the butter in a pan on the stove over medium low heat until very soft.
Once everything is cooked combine the spaghetti squash noodles, chicken, onion, yogurt, 1 cup of the cheese, salt and pepper in a large bowl.
Place the mixture back into the empty shells and top with the cheeses and place under the broiler until golden brown.