I am using a similar setup to what you are asking. I did not have the JBL system in my truck, but I upgraded the stock 6-disc in my truck. I custom built a box to fit into the small drivers side compartment that is similar to the Tacotunes box in dimension. I changed a couple of dimensions to get a better fit for what I wanted, but it came out great. The single 10" has plenty of bass, and sounds awesome. I still have a small amount of storage space at the bottom of the large compartment, but the amp rack has taken up some of that space. Here is a couple of pics...

 

^ Nice clean set up. I wish the Access Cab had that much room. Oh well, I'll figure something out.

 

Hey Roboots, did you ever calculate the AIR SPACE in that box and the MOUNTING DEPTH? I am considering the same set up.

 

For the dimensions that I used I get 0.53 cu. ft. of AIR SPACE in the box (can easily be made to appear larger with some poly-fil or acousta-stuff. The MOUNTING DEPTH is ~5". You will need a shallow sub for this box to work, but it can still pound out some excellent bass. Let me know if you need any thing else. Thanks!