3 batteries and ho alt, necessary?

I am already planning on buying a HO alternator --- Im going to get it custom made through a dealer here - Also I will be doing the Big 3 upgrade as well.  Now since I already have the two caps why would I ditch them?  Do they not help the system?  Im still getting another battery and the HO alternator...since I have them should I use them?  Or if not could you explain why not?  Its not like im going to go out and buy them...I already own them lol.

Now back to the question about that paritcular Isolator...since I really really dont want to buy two new batteries since I have one, my batteries wont be identical.  Reading that artical that he linked clearly stated that the two batteries must be identical and within about 6 months of each other - correct me if im wrong please.  So since my batteries will be 1 year apart I will need that isolater will I not?  If so is that isolator sufficient?

P.S. Im not trying to bash what you all are saying but Im trying to get all sides to it, so when I make my final decision I know 100% that I made the right one.

Thanks again for all the responses.

haemphyst thanks for that info - I am now considering your other alternative lol.  But I now have to ask why NOT the Yellow Top?   Whats wrong with the Yellow Top ones from reading their site it looks like they recommend their Yellow ones for car audio instead of the red ones?  So are you recommending I get rid of my Yellow Top Battery and instead purchase two Red top batteries?  One for under my hood and one for the trunk?  Or would you recommend the batteries made by Kinetic - I have heard very good things about them.  Either battery I decide upon I would then connect them both to my custom made HO Alternator like that post that I was refered to previously.  Am I correct so far?  That way I dont need to purchase an isolator / solenoid.

I made this very bad sketch of how I envision this two battery set up --- All wiring shown would be 0 gauge wiring.

(Please forgive the sizes of the batteries to the car and alternator.  I am not an artist!)

Also all the wiring for the Big 3 upgrade would be 0 Gauge as well am I correct?

Lastly any idea of how many amps my custom alternator should be putting out?  Thanks.

Well thats alot of white space that I wasnt expecting...opps.  Well then hopefully this link will work...I dont want to run into that problem again...waste of space.

Here is a link: https://i75.photobucket.com/albums/i320/twobig86/DiagramforBatts.jpg

Thanks again for all the advice Haemphyst -  I have been away on a white water rafting trip so thats why I havnt checked in over the weekend...btw if you like outdoor stuff and adreneline rushs whitewater rafting is for you lol.

Anyways I have given in and will be purchasing two red top batteries when I set my system up.  I thank you for all your advice as it was extremely helpful. 

Still the only thing that I still dont know is how big should my custom alternator be? 

Those 3 amps have 250 amp fuses combined

100 amp fuse + 100 amp fuse + 50 amp fuse = 250 amps

250 amps * 14.4 volts = 3600 watts

Am I right so far?  Anyways from here I dont know how to go.  I dont know what type of car I will be purchasing either so I dont know how high the HO alternator for that car is.  However im thinking I will need to do the custom one anyways.  Any help on an approximate amperage for the alternator would be great.

i came across this on a website and thought it was interesting since there seems to be some conflicting agreement about the yellow top vs red top. 

"The Yellow Top is still a decent starting battery but due to a different chemistry for the paste material on the plates and a stronger acid it has a little less starting power than the Red Top" 

i guess i was just in the market for a battery and one said redtop and the other said yellow.  it was 50/50 so it made it a little hard to jump the fence on which one to buy.  anyway what do you guys think about the statement above?