kinetik or yellow top optima

whoa.  there isnt a single period between what looks like 5 or 6 sentences. that was a mouthful, and hard to make sense of. ill give it a go though

your alternator can only supply so much power. the more batteries and caps you add, the more voltage drop youll have. thats more of a strain on your alternator. i do believe that kinetik batteries are a better choice than optima batteries (for people with large systems). however, if you are getting voltage drop (i know you already upgraded your alternator) you may need a larger alternator. however, i do not know all the specifics of your amperage draw and the components you have. if you just have that one JBL amp then what the heck do you have 3 batteries for!! if you have a lot of other equip that you didnt list, then its hard for us to recommend anything for you.

if you just have that one amp, i would uninstall 1 of the batteries, and uninstall the capacitor. these are making the load on your alternator worse, and are not necessary for a system with just 1 amp. this may help a bit.

otherwise, give us more details

well i am using 2 amplifiers 1 4 channel power acoustik 100x4 rms and the jbl 1200.1. i am not using a battery isolator i thought that was only for when one battery goes bad u can still start the car am i wrong?what other things can they be used for.

wow - you have more batteries than you have amps!

get rid of one of the batteries and the cap. your alternator is not popwerful enough to keep 3 batteries charged. im not even totally sure you "need" two batteries at this point, although it might not hurt anything.

im saying all this assuming that the two amps are (for the most part) the only significant power consuming aftermarket electronics in your car.

now if you have an SUV with a winch on it, light bar, playstation, multiple tv's, etc... then that may be a different story

as for the battery isolator only being to isolate the two batteries so you can kill one, and still have the other to start your car... well, that is partially true. this is one of the main ideas behind it. but its not the only  one. however, i think that velocity motors or tcss could explain it better than i could, as im sure they know more of the specifics than i do. its been some 5 years since i quit my job as an installer.

your only using two batteries? i was under the impression you had two under the hood and one in the trunk. your first post was not very clear

The batteries only power the system when the car is not running- and I doubt you play it full bore under these conditions.  If you have not already done so, you should upgrade your alternator to the one that puts out the most (hot rated) amps at idle for your car.