IMO the JL is a better all around sub. Square subs have stress points that cause them to be very unreliable. I also feel that their sound quality is not on par with the top end round subs. If I was you I would go with the JL. The W6 V2 is a great sub, and with 2 of them I am sure you will be happy. As for your amp, I beleive it will work just fine. RMS is 1000 watts at 2 ohms, so with 2 w6s it should work just fine.
Me too! Go with the Jl
f*** that, go with the solobaric man, that sub will bang the hell out of your ride