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Yep. On a stock alternator and only 1 battery. You must be really optimistic about the ability of his "20f capacitor". Seriously, if you're not going to offer to repair, replace, or handle warranty when some rookie breaks his amp that's really ****** advice to throw out.
I can take a battery from your cordless drill and touch the speaker wire to the pos and Neg and the cone should either push out or svck in and then do that to the other Woofer and make sure they are both going the same way. Make sure they in phase with each other.
Just a flashlight battery or 9 volt will work here as well. Simply pull the speaker leads out of the amp terminals and touch the two sides of the battery to the two leads and see which way both speakers pop in or out. They should move the same distance and in the same direction.
I'm going to guess that the box is a huge problem. That's simply not enough port area or box volume for a pair of 12's.
That box should probably be scrapped or build a new baffle and try some 8's in it or just a single 12. Personally I wouldn't even try smaller subs in it since that port is just tiny I'd worry if it would even perform properly for smaller subs, or what other problems it has.
Poly-fill isn't the silver bullet to make subs work in half the volume they need. It can flatten out peaks in frequency response (like a bigger box would) but it won't give you the extra output/efficiency. Generally if you're not building a transmission line or have some other compelling reason to use batting it's a band aid that's inadequate to fix a far bigger problem.
Lastly, I think OP rather walked into it by claiming he tested the subs being 1 ohm, then reneged and claimed they were dual 2 ohm. WHICH IS IT!?!?