Upgrading the alternator is massively expensive, vehicle warranty-voiding in many cases, and in many cases - fundamentally deceptive.
Not something to be entered into lightly - to spend hundreds of dollars on a '200a alternator'... that doesn't make it's "200a" until something like 3000RPM, when that alternator perhaps has a similar current output at idle that your stock alternator did - or worse, even less! //content.invisioncic.com/y282845/emoticons/eek.gif.771b7a90cf45cabdc554ff1121c21c4a.gif
Not to mention - if you have enough power in your car to seemingly warrant an alternator upgrade, and you can actually stand to be in the vehicle - there's a much larger scale problem at hand than an alternator that isn't large enough - you've got some serious efficiency problems, that can be caused by numerous things - whether that's enclosure size for subwoofers, or inadequate baffling for main speakers. //content.invisioncic.com/y282845/emoticons/wink.gif.608e3ea05f1a9f98611af0861652f8fb.gif
Adding an auxiliary battery, on the other hand, can be done on the cheap... no isolator required even, just hang it off your distro block in the rear, let it help supply current, and augment the key-off run-down time of your car naturally.
And don't use a deep-cycle battery for the rear battery - they are built more durable via the use of thicker plates in the battery - which make for slower transient response - transient response being something batteries are already inherently slow with, even non-deep-cycle types.
To that end - if something along the lines of light dimming are your symptoms..
Perhaps neither the battery nor the alternator would be truly suitable upgrades!
You may exceed your alternator's amperage at some RPM, with some music, at some output level regardless of alternator size, or even quantity.
And the battery really only helps augment either key-off time, or filling in for those times that the alternator can't supply the current alone.
So what to do?
Much of the drama of the light dimming is caused by that transition period, the brief moment in time where the alternator can't supply all the voltage, and system voltage is falling to the 12v level of the battery, and then the battery rising to respond to augment the alternator (the transient response I spoke of).
If light dimming drama is embarassing, adding a capacitor can be the utopian upgrade.
They can be had for under $50, they begin augmenting the moment the voltage begins falling, and have adequate charge to cover the milliseconds worth of transition period until the battery does rise and take over augmentation duties.
At this point - is it too much to ask - why are you considering upgrading either?
ie. What are your symptoms?