Our alternators are underpowered as all hell. You can try to fix the problem by grounding the "big 3" ground wires with some 4 guage wire (rather than the stock small wire) to get a bit more out of it. You can also hook up your amp to a capacitor to level out the voltage a bit for you, so you don't damage your amp/sub when you hit bass notes.
These, however, are cheap fixes that do not address the real problem. In fact, they may get a bit more power out of your existing alternator, but they can actually do damage to it by doing so. Our trucks need more amps! Try to find a high output alternator.
Good luck.