I got a JL audio 6 channel amp to replace the stock bose amp but it never occured to me about the nav and blutooth voice. I am keeping the stock HU and just replacing the amp in the trunk,

I assumed they both fed into the head unit and were fed to the amp over the normal 2 or 4 channel inputs to the amp. I am looking at the factory wiring diagram and it looks like the tel unit feeds directly to the amp.

Am I trippin or am I screwed?

 

you sir are correct. if you only swap out the amp then you will be fine