I am looking at installing 2 of the JL 12Tw3's under my rear seat and I am trying to figure out what would be the best amp for them. I am thinking about the JL Jd 1000.1 but worried overdriving them

 

This is the wrong subforum, but I'll help you out until a mod can get this moved. Those speakers are rated for 400 watts at 4 ohms. That amp is rated for 600 watts at 4 ohms, so it's over powered for those speakers.

Sticking with the JL JD lineup, your best bet is the JD 500/1. This will give you 250watts to a single channel at 4 ohms which is well within the recommended power range of 100-400 watts for those speakers.

https://amzn.to/33QYqrq

 

I thought the JL 500.1 was only 250 @ 4ohms
That is why I was thinking 1000.1 and turning the gain down

 

If you are talking about the 12TW3-D4, those subs have dual 4 ohm voice coils. If you are using two just wire the voice coils in series on each sub which will make each one an 8 ohm impedance, and wire the pair parallel to the amp. It'll be a 4 ohm load so 600W total to the pair or 300W apiece.
https://jlaudio.zendesk.com/hc/en-us...bile_site=true

 

Yes the JLW3D4 2subs in series parallel running a 4ohm load to get clean bass sorry should have been more specific