Had this happen once before...had the battery tested...was fine,but i changed the alternator cause i had one laying around...

Well it came on again...shortly after i hooked my sub and amp back up...same thing that happened last time.So i take it it's my alternator again right?

I don't know what kind of alternator you have (amps) but it sounds like you are running an amp that uses more power than your alternator can provide. What you could do is - with the car running - test the voltage at the battery terminals - then test it with the stereo system on, when the bass hits - if it drops below say 13 volts you should get a high output alternator. Don't bother getting a capacitor - they're a waste of money and store almost no power at all. You should also look into doing the big 3 modification. Better grounds are essential to your charging system.