I plan on putting my 2 12" JL W3's this weekend, i was wondering if i should leave the stock sub plugged in or not?

Im replacing the 6x9's too.

 

Well, if you have a tl 04 or later, then you have 6.5 in in the deck with the stock 8" sub. you should search these forums about this topic. There are only about a million posts. You will find easiest install to take line level straight from sub to a LOC (line-out-converter), then RCA to your aftermarket amp. You will should disconnect so you don't get interference between different sized subs (which u will get)!

 

Do you have a 3G TL? Where are the 6x9s located?