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It is filled up by killing other demons who souls go into the cube. You have to use a different weapon to kill normal demons in order to fill up the soul cube. To do this simply strafe around the edge of the hole and kill demons as the come up. Be careful not to let them overwhelm you.    You just beat the game!
You got the soul cube earlier on in the game. When you first begin the fight, do not use the soul cube. It takes five kills to fill up the soul cube  Once the soul cube is full, "aim" it at the Cyberdemon (you want to hit him, not waste it on a useless target like some imp running around)  To kill the Cyberdemon, you must simply hit him 4 times with the Soul Cube. Sit back and watch the end cut scene.