Prep the squash: Preheat your oven to 400°F (205°C). Carefully slice the spaghetti squash in half lengthwise and scoop out the seeds.
Brush cut sides with 1 tablespoon olive oil, and season with salt and pepper.
Roast the squash: Place squash halves cut-side down on a parchment-lined sheet pan. Roast for 35–45 minutes, until the skin gives when pressed and strands pull away easily with a fork. Set aside to cool slightly.
Pound or slice chicken: If your chicken breasts are thick, slice them horizontally or pound to an even 1/2-inch thickness.
Pat dry and season both sides with salt, pepper, garlic powder, and onion powder.
Breading setup: In one shallow bowl, whisk the egg with a splash of water. In a second bowl, mix breadcrumbs with Italian seasoning and a pinch of salt. Dip each chicken piece in egg, then coat in breadcrumbs, pressing to adhere.
Cook the chicken: Heat a large oven-safe skillet over medium heat.
Add 1 tablespoon olive oil. Sear chicken 3–4 minutes per side, until golden and just cooked through. Remove to a plate. (Alternatively, bake breaded chicken on a wire rack at 425°F/220°C for 12–15 minutes.)
Shred the squash: Use a fork to pull the strands from each squash half into a large bowl, keeping the shells intact if you plan to use them as “boats.” Season strands with a pinch of salt, pepper, and red pepper flakes if using.
Warm the sauce: In the same skillet used for chicken, pour in the marinara and bring to a gentle simmer.
Nestle the cooked chicken into the sauce. Spoon some sauce over the top.
Assemble the bake: Either: Boat style: Divide the squash strands back into the shells. Spoon some sauce onto the squash, top with chicken, then add more sauce.
Skillet casserole: Add squash strands straight into the skillet with the chicken and sauce.
Toss lightly to combine, keeping chicken pieces mostly on top.
Add cheese: Sprinkle mozzarella and Parmesan evenly over the chicken and squash.
Melt and brown: Place under the broiler for 2–4 minutes, watching closely, until cheese is melted and lightly browned.
Finish and serve: Let rest 3–5 minutes. Garnish with fresh basil or parsley. Taste and adjust salt and pepper.
Serve hot.