You do not need to upgrade the battery or alternator and the 'big 3' is usually a waste of time and money. In your situation, it will not make a lick of difference as far as output goes b/c it's a regulated amp. That means the amp will make the same power over a range of voltages and adding 'the big 3' will net somewhere below 1v if your factory wiring was poor (which it isn't).
If you want more output, throwing power at subs is the wrong way to go about things. Sure, power is cheap but all the additional accessories (big 3, fire hose power wire, etc) adds up quickly. Additionally, throwing more power at a speaker does not always mean it will be louder. If, say, 250w is all that is needed to reach the mechanical limits of your subwoofer adding more power will not make them move more air. Things don't work that way. You'll sound a little better, but not louder.
It seems like you're not satisfied with those subwoofers. If you have a garden variety sealed box, I'd look into replacing those woofers with something that can either move more air -or- does more with less power (efficiency). A proper vented box for a pair of 12's is HUGE and that puts a lot of people off.