Preheat the oven to 350 degrees F (175 degrees C).

Place squash halves, cut-sides down, onto a baking sheet. Add enough water to come 1/2 inch up sides of the baking sheet.

Bake in the preheated oven for 40 minutes. Drain off any remaining water.

Meanwhile, melt margarine in a large skillet over medium heat. Add apples and onions; cook until onions softened and turned translucent, 10 to 15 minutes. Transfer mixture to a bowl to cool.

When squash is cooked, stir Cheddar cheese, raisins, brown sugar, and cinnamon into apple mixture until evenly combined. Flip squash halves on the baking sheet; fill cavities with apple mixture.

Bake in the heated oven until filling is hot and cheese is melted, about 15 minutes.