Preheat broiler. Cut squash lengthwise in half; discard seeds. Place squash in a large microwave-safe dish, cut side down; add 1/2 in. of water. Microwave, covered, on high until soft, 20-25 minutes. Cool slightly., Meanwhile, in a large nonstick skillet, cook and crumble sausage with onion over medium-high heat until no longer pink, 5-7 minutes. Add garlic; cook and stir 1 minute., Leaving 1/2-in.-thick shells, scoop flesh from squash and stir it into sausage mixture. Place squash shells on a baking sheet; fill with sausage mixture. Sprinkle with cheese., Broil 4-5 in. from heat until cheese is melted, 1-2 minutes. If desired, sprinkle with pepper flakes. To serve, cut each half into 2 portions.