Ok, this is basically how it works boys and girls,
The Magnuson-Moss Warranty Act was passed in order to protect those who have modified their cars, as well as car companies. The concept is pretty much this:
If the dealership can prove beyond a reasonable doubt that your aftermarket product had a direct relationship to the problem which occurred, they can void your warrenty on the part/system and refuse to honor the warrenty.
However, if you have aftermarket parts that are unrelated completely to the problem at hand, the dealership is required by law to honor the warrenty, and service the vehicle.
Also, if you get work done by a shop, such as an audio install with a high wattage or amperage draw(electrical system), or an aftermarket muffler system (engine/exhaust), I reccomend that you keep your receipts. Most dealerships will just say "gah, fine" and do the work if you come in prepared with all your information, and can prove to them that the aftermarket work is done by a professional.
oh, if I made any mistakes, pm me and I'll edit this.
The above is my interpretation of the Magnuson-Moss Warranty Act.