always battery first. there are two reasons why.
1) Stock batteries in cars simply cannot deal with 1000Wrms+ of power, lower amounts are acceptable but will kill the stock batt eventually. This is simply due to the design of the battery itself, most stock batteries are designed to start the car by giving one large burst of power and then be continually charged by the alt. After starting, these batteries are only designed to give approx 35A of output constantly for any given time. When you upgrade the battery you will but a deep cycle battery in place of the stock starting battery. These deeps cycles are for a large amount of current draw as opposed to the smaller 35A draw, they can also be drained and charged with no ill effects. Basicly, they are designed to a car audio type application.
2) Music is dynamic, therefore the current demands required by an amplifier isn't as detrimental(sp?) as opposed to a tone. For every bump by the subs there is a time when they are quiet, giving the battery a chance to draw on the alt to charge back up. generally this is enough time for the battery to recover, and since it can catch up there is no need to replace the working alt.
now, you are going to hear a lot of people say "you are going to overwork your alt and kill it much quicker than you normally would." The catch is, you will notice a difference if you add a deep cycle battery (not an alt), if you only add the alt there will be zero difference because the stock battery will not have the current on tap that is needed for higher powered systems. So, you can buy the batt now and the alt down the road (worst case possible), or you can just buy them both now (and maybe not need the alt at all).
edit: by the way. my truck = 3500Wrms w/2 yellows and 150a alt. I have to push everything hard for a good 5-8min to even get dimming. Didn't even do the big 3, just an extra ground for the batt.