It's an AP3k man... One good battery is enough. You more than likely have a 120a alt (double check). Figure you have 50a in reserve and your amp draw with that amp is 200 MAX. Figure less than that unless it's an extreme situation (voltage drop, clipped out the ass, etc).
Hook up what you have and see how it does. If it sucks (voltage wise) get a good battery and sell the cap. Just remember if you want to go 14v+ all the time you're going to need like a 300a alt especially if you have another amp for interiors.
If I were you I would do what I said, hook it up and see what happens. If it doesn't work well sell the cap, get a 3100 or 2400 or 2700 (whatever fits) and a smaller one for the rear if you still need more. Just keep in mind you can't run around blasting it all the time even with an alt, it will fry.
So should I use the cap for now? And if it sucks then take it off and get a big battery? Or what?