I am about to get a hold of 2 12 JL W6's (old version) and a 500/1 Amp with no box and I am curious as to where I can find a good dual box for both of these. JL recommendations are here (https://www.jlaudio.com/subwoofers/pdfs/10_12W6_MAN.pdf). Also should I look for a ported box or a sealed one? Which would sound better? On that subject should I wire the subs in series or parallel? This is going in to a 97 Le Pathfinder if that makes any difference. Onto my second question will my battery be able to support the 500/1 amp? Should I look to buy a cap with the system? Any help would be great.
Is your amp 1 ohm stable? That is the burning question.

You either wire the coils in parallel like shown here, or your other option is a 6 ohm load. It boils down to what the amp is capable of, and the power you take from the car has everything to do with how the subs are wired.
Note in the manual a big difference in enclosure volume between ported and sealed. You would measure your available space to find out if you have the cubic feet of room needed. After that, it's a matter of personal preference.
There are some prefab boxes that are suitable for sealed, but if you are going ported then you should have one custom-made.
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Build the box so that it performs well in the worst case scenario and, in return, it will reward you at all times.