Thanks for responding,
I finally gave up on trying to find a hole through the fire wall and drilled one last night. Yes, I do have my power cord running from the battery to my amp (with of course the fuse box next to the battery). But now I have run into a problem! Everything is hooked up as it should, I will explain how it is set up.. I have the amp remote wire intercepting the ACC (accessory) [red wire] connecting to the stock head unit. I found a similar schematic seen here: http://carstereohelp.net/wireharness_Lexus2.htm
After that, I connected the RCA's running out of the amp to a RCA converter (which converts RCA cables to speaker wire) I then intercepted the speaker wire with the 8' Stock sub in the trunk.
Now when I connect the power cord to the battery with everything else hooked up.. The POWER and PROTECT lights flash on my JL amp and then turn off right away.. I don't understand where I went wrong. Please help.