Whats the total amount of fuse size(s) in your total amount of amplifier(s)? That will tell you the draw rate of your system and you should plan for it accordingly. I.G. Two amplifiers, One mono block amp with four (4) 40 amp fuses has a potential draw of 120 amps, the second amp may have two (2) 20 amp fuses; a total of 40 amps. Together that is 160 amps of "rated" current draw and you should plan out that the stock alternator is 95 amps, and although 120 would be better but still not enough to keep your system at peek charge all the time for very long ESPECIALLY if your charging at least 2 batteries.
I would suggest one of two things, both will save you money short or long term. Short term would be redesigning your system for a realistic sized power and budget based upon cost factors of shortened life of Batteries, Alternator, possible multiple electrical system failures or electrical gremlins. If you have a disposable income and like replacing alternators and batteries every other year in a leap-frog type manner, Please.. Dont let me change a thought.
Long term would be to invest in a custom alternator meant to handle the minimum requirements the truck will need, Plus your systems needs (with two brand new matching batteries), and a tad more so you can keep an adequate charge all together. Most important if you are using amplifiers with "unregulated power supply's". The difference is this; A Unregulated power supplied amplifier will increase/decrease power out put based upon input power voltage. so if your amplifier say was putting out 200w X 2 @4ohms @ 12.4 volts but if you were to increase your input power to 14.4v because you have more power going in, that same said amplifier may give you 265w X 2 @ 4ohms @ 14.4Volts. If it was regulated power supply, no matter whether you had 12.4v - 14.8v input the amplifier would remain at 200w X 2 @4ohms regardless.
Another thing, The capacitors ideally are misrepresented and where they should be at in a system design because of how they "Actually function" VS what people have been told in most cases. They should be used in conjunction with your mids and high amplifier as a filter to help clean up the harshness of the higher frequencies and tighten up the midbass and lower bass. Sub bass itself IS A DISTORTION and with a Class D amplifier adding a capacitor to it would be a waste of effort and time.
Rule of thumb, 1/2 farad for every 250 watts. and if your pushing 500w RMS ( I hate that word cause in reality it doesnt exist but), your better off with two 1/2 farad capacitors inline than 1 single farad cap. One critical parameter of capacitors (and what differentiates a poor one from a better one) is its ESR (equivalent series resistance.) Look for caps with the lowest possible ESR. This enables them to charge and discharge faster (and thus perform better in high frequency operation.) Cheap caps have poor internal construction and higher ESR values. The most common method for determining capacitor failure is measureing high (sometimes infinity) ESR. You need a specialized tester to measurte ESR, by the way. It cannot be done with a standard multimeter...
On another note, Id suggest removing the bottle neck starting at the alternator; Meaning I would run the best grade of Copper audio wire your willing to afford. I think a 1/0 from the alternator to the fuse box (ill add some pics to this later) and distribute to the battery. If your going to go dual battery setup then 1/0 to both batteries will be necessary. Upgrading all the standard 6ga cables in the battery wiring to a 4ga would be ideal as well as upgrading all the underhood grounds from the engine to the chassis, hood to firewall (passenger side of truck) and the few intake manifold to block grounds. This alone should be a tremendous LESS strain on the electrical system and lessen those dimming lights.
Remember !! Electrons flow from positive TO negative.. NOT the other way around. And just so your aware of how current flows through wire, it travels on the outside of the wire, NOT like you would think water would flow through a pipe. So the better grade of wire or copper the deeper into the wire and BETTER current flow you will have thus upping your performance electrically. No sense trying to have a vehicle as fast as a Ferrari if its gonna stop like a 73 pinto.
my $.02
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Also, for the difference in functionality, Red top Optimas would be the better way to go unless your baller and want to go for the Kinetic batteries which I think may be the better route but def more money.
http://www.kinetikpower.com/2009/default.asp