I'm fairly new at it myself but the only advice I would give is to make sure you only put the microwave on 50% power for about 3-4 minutes and stir, stir, stir. then heat in 30 second intervals until 340 degrees. 360 or so and the smoke will drive you out of the room.
Polycarbonate molds don't last as long because of the heat, so aluminum would be better. I know you are doing this to save money but if you are having trouble matching the color you want, you can always go to the store and buy plastic baits at Walmart or somewhere cheap and reheat them.