New Alternator Wiring With 2nd battery

[GoldSilverEagle]

Hello Everyone,  I have a 2000 LS400, I installed a GPS double din head unit, pioneer avic-8100nex, best head unit ever, especially for this vehicle. I also have a 1000 watt 4 channel, amp, and a 3000 watt sub amp.  Alpine 250 x 4 running Focal components, And 2 Sundown Audio X10 10" each running 1500 watts rms and sundown audio 3000 watt amp, Pushing 3000 watts at 1 ohm.  
 Thats just a background,  I also have a second battery in the trunk, optima yellow top.  My alternator went out, which i was expecting, and i had it rebuilt to 220amps. So I added some wiring when I installed everything, and wondering if everything is correct because now I need to replace my main battery, I believe so anyways. Everything was running perfect for exactly a week. Then My 3000 watt amp shut off while idling. and I noticed my battery light blink. when I got on freeway all was fine, 3000 watt amp turned back on etc. I went to napa to have battery tested and it showed 10.3 volts and 200cca out of 600cca, I had left the car running ....Just wanted to get home when I heard that. He said to disconnect wire connecting batteries to get ideal readings. I figured I'd take them both out and test them out of the car. The underhood battery was already in the car when i bought it 18 months ago. I assume this battery needs to be replaced regardless, I hope I didn't damage the Yellow Top, If thats even possible?

                                                                      but here's how I wired it. 
         
                                 This is factory 

Alternator = factory 6 gauge goes to under hood fuse box,  Then From Fuse Box factory 6 gauge goes to positive battery Terminal.

Ground  = Engine Block to Chassis To Negative Terminal on Battery. 
       
           
          
                 My Additions are just that, I did not change the factory Wiring, 

Alternator = 0gauge/1ought wire from Alternator Straight to Positive Terminal on Battery
Ground = 0gauge/1ought from Enginge block, to Chassis to Negative on Battery Terminal
Battery underhood=
                 Positive Terminal = 0gauge/1ought wire to Battery in Trunk Positive terminal 
Battery in Trunk = 
                 Positive Terminal = 4 gauge to 1000 watt 4 channel amp under passenger seat where factory amp,Ground to Chassis
                                                0gauge/1ought Positive Terminal to 3000 Watt Amp
                             
                  Negative Terminal = 0gauge/1ought to Chassis
                                                   0gauge/1ought to 3000 watt amp Ground

Main questions are=  *Wiring straight from Alternator To Underhood Battery to Much/ Overkill? Or even Necessary? 
                                  *2nd Battery in trunk, should It be identical to underhood battery? Or keep Yellow Top And Add a Battery Isolator?
                                  *Should I run 0gauge/1ought from Alternator to Trunk Battery, And Remove Ogauge/1ought that Connects Batteries?
                                  *If I keep Batteries Connected with 0gauge/1ought, Should I run Negative 0gauge/1ought between Both Batteries? 
                                  *Something else I should Test? 

I apologize it's so long, I like to be thorough and include all information I have.  If there's something I missed, please let me know and I will reply asap. My intentions are to handle this later today.   Thank You for reading
 

[The Wrench]

Hi there Jeremy.

I reached out to an expert in the field for you. here is his answer to your question.

Dude needs to add capacitors. He probably pounds the subs. They are drawing too much current to satisfy all of his power-hungry components. In addition, adding another yellow top to the back would help shoulder the load. And the closer the stiffening caps are located to the sub amps, the better.

Hope this helps.