your lights will dim every time your bass hits if the amp is kcking high enough power regardless of the alternator size. of course its going to say low output because its drawing a lot fo power from it to power your subs.
do you have a capacitator installed/installed in the right place in the circuit? if not, that's probably the problem. if theres one installed already, the higher output alternator may help and you should get a thicker gauge wire to handle the extra current just incase