Sure, depends how much you draw on them. Having an extra two batteries doesn't do anything bad. When you drain all of your batteries really rapidly though and the stock alt can't keep up to recharge them, that's when you have problems.
Basically, if you're running X amount of power on 1 battery and stock alt. You might be exceeding the battery's output and all the strain is falling directly on the alt (bad...) Adding more batteries will slow the rate at which the voltage drops, but you're still drawing X amount of power that has to be replenished at some point. Having a few batteries is better than not, but you should upgrade your alt.