How to get the best out of my subs?

I have 2 12" kicker CVR subs. They are in a box with a frame missing but I put that part down so it's some what sealed. I just hate hearing that bad sounding bass. On one song there's one bass note that hits lovely but the others kind if sound like ****. I have them hooked up to a 1200 watt kicker amp. I use an alpine amp and USB to my iPhone.
Suggestions?

You will have to get a new box