Red is really good for starting in cold weather.
Yellow is better at running for longer periods with the car turned off running stereo or accessories....and still being able to start.
As for Caps:
Go to Caraudio.com and go to the forums. There are HUGE debates on Farad Caps. Almost all competitive people do not use them. They go with the "Big Three" first, then add extra batteries as they see fit. They basically see farads as band-aids to a poor electrical system. They help cover a problem, but do not solve it.
Personally, I have a 5f cap running in my other car that is running close to 1500w rms. I went with the cap because really I am too lazy to do the big 3. I did see an improvement in the dimming of the light issue's I was having when I installed the cap....but who's to say that if I did the big 3, maybe they would go away too.
As of now....the FX has a pretty stable electrical system...I would hook up the stereo with the big 3 with a yellow top and see if that can handle the voltage you want to run.
Turbocad used to compete in SQL. I'm sure he can provide you with a detailed

wink (2)

explanation of what to use and why. He is very informative about car audio.