It all depends on the power ratings of the subs you decide to go with.
Now going off your original post...here is what i would suggest:
If you get the JL W3v2's (I however would recommend getting a single 12in JL W6v2. I currently have that in my car along with the JL 500/1 and it is plenty of bass. Check out the reviews at Car Audio and Electronics. They rated it the best sounding subwoofer they have ever heard. Definitely seems to be underrated when compared with subs of different brands such as Alpine, Rockford Fosgate, and MOMO.) - stick with a 500/1 to power them both. 1000 watts is going to be too much power especially in the upper levels. I know for a fact that a JL 1000/1 can blow out even a gently used W3v2 and have seen it happen first hand (that's another story though).
If you get 2 Alpine Type R's (depending on your price range you might be able to afford the new Type X)- you might be able to get away with a 1000 watt amp. It is going to be a lot of power for the Type R's to handle but from what I have heard they are definitely sturdy subs. If you are truely worried about your investment and do not have a warrenty...go with the 500 watt amp. You wont have to worry about blowing out the subs. Also if you dont upgrade your components, the 1000 watts of bass is going to overpower them with ease.
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