charging system problems

i just bought a 93 acura integra and did an engine swap (dropped a 91 integra GS motor in it) and my charging system light keeps coming on and off at completely random times, i have installed a subwoofer and connected the power cord directly to the battery, and when the charging system light comes on my sub shuts down, i am thinking it there might be a problem with the altenator but i am not totally sure, in about i week i am going to have time to take it out and test it, i was just wondering if anyone else might have another idea and/or solution to my problem.

i just bought a 93 acura integra and did an engine swap (dropped a 91 integra GS motor in it) and my charging system light keeps coming on and off at completely random times, i have installed a subwoofer and connected the power cord directly to the battery, and when the charging system light comes on my sub shuts down, i am thinking it there might be a problem with the altenator but i am not totally sure, in about i week i am going to have time to take it out and test it, i was just wondering if anyone else might have another idea and/or solution to my problem.

do you have a high power amplifier hooked up as well?

i wouldn't call it high power, it is only 550 amps, but i have recently been told by a friend that it could be the voltage regulator in the altenator, i am gonna have a ton of fun checking that out