Man you need someone to explain the entire basics for you.
That deep cycle in your trunk is a flooded battery it will never be the same as a decent agm battery.
The alt you bought is likely only putting out decent amperage at high rpm. Car audio alts run smaller pulleys so at idle the spin the same speed as a regular alt at high rpm. This lessens the life span of the alt but you get alot more power at low rpm.
Rockville is a budget brand and never makes the power they state on the box, the subs aren't going to take 3000w rms either.
A 4 farad capacitor is only going to benefit you if it's installed on the headlight circuit. It is no where near enough power storage to be beneficial for a sub system. A super capacitor is a different story and they often start at 500farad and are the size of a battery.
Autotek hasn't been worth much since the maxxonics buyout.
My suggestion to to pick up one of those amps first recommended because you don't have the electrical to supply 300+ amps to a 3000w amplifier.
I didn't even look at the wiring you have but if you don't have a quality 1/0 power cable ran from the alt to the batteries both front and rear you don't have anyway to support 300amps of power draw.
You can use distribution blocks to downsize the wire in the trunk, or just use your rear battery post.
My honest suggestion and one you can do in steps is
1. Replace that amp with the sfp1500
2. Build a custom box designed by someone like
@Buck or
@shredder2. I would not bother building a box for those Rockville speakers but you can use those speakers as a fill gap.
3. Pick up any decent 750-1000w rms sub sundown sa series, incriminator lethal injection, digital designs 2500 series, daton ho or ultimax, pretty sure ssa makes one as well as fi caraudio.
Pick the subs you want as an end goal and have the box designed around those subs. That way you can swap the Rockvilles at any time and have a custom enclosure for the new better subwoofers.
Lots of good amp companies out there but you often get what you pay for. I personally like ddaudio amps but they are rather expensive