Preheat an oven to 180 C / Gas 4. Place the squash onto a baking tray cut side down. Fill the baking tray with 1.25cm of water.
Bake the squash in the preheated oven for 40 minutes. Drain off any water remaining in the baking tray.
While the squash is baking, melt the margarine in a large frying pan over medium heat. Cook the onion and apple in the margarine until the onion has softened and turned translucent, 10 to 15 minutes. Scrape the mixture into a bowl to cool until the squash has finished baking.
Once the squash is done, stir the raisins, light brown soft sugar, cinnamon and Cheddar cheese into the apple mixture. Turn the squash cut side up on the baking tray and fill with the apple mixture. Return the squash to the oven; bake until the filling is hot and the cheese has melted, about 15 minutes.
If acorn squash is unavailable, substitute in butternut squash.