2 12w6v2's would be properly driven with a 1000/1, but you can definitely still run the 500/1 if you want. I ran 2 10w6v2's with a 500/1 and it sounded fantastic...but yes, you will probably want more sound out of them than you'll get with the 500/1, causing you to crank the gain, causing the amp to clip, causing the subs to blow. If you're going to drop the dough for the w6's, go ahead and give them sufficient power, even if it's not JL power. Gain does NOT equal loudness, that should be set before speakers are even hooked up and never touched again. Here's a quick tutorial on how to properly use your gain settings:
http://mobile.jlaudio.com/support_pages.php?page_id=143