I am replacing my 2005 double cab stereo with a double din stereo. I purchased the wiring harness to plug into the factory amp/steering wheel controls. I also purchased 4 polk audio db651 two way speakers. The front stock speakers have two sets of wires running to the three door speakers. I have looked everywhere for a solution to bypassing the amp. How do I wire the stock setup to two way speakers. I understand I can bypass the amp, but would rather not. Thanks for all your help!

If I were you, I'd bypass the stock amp and use the internal amp of your new head unit. If you have the same JBL premium system that was in my '05 Sequoia........then there is really no easy way to do what you are trying to do.
In mine, the oem amp controlled fading, and there were only one set of outputs from the oem HU to the oem amp. That, coupled with the fact that the oem speakers are a mix of odd Impedance loads.......you could damage your new speakers, the oem amp, or both.