The only way a modification will void your warranty is if the modification causes the problem. Even then it is supposed to be up to the dealer to prove that the mod caused the problem. If you install a new head unit it might void any warranty on the speakers and the amp but that should be about it. It's not going to affect your warranty on the engine, transmission, etc. Of course that's assuming you installed it correctly and it doesn't short out the electrical system or something like that.