say I want to replace my stock CD player, I have the BOSE premium system, will it all work if I just put in a new CD player or I will have to mess around with the system?

 

Yes... and look in the right forum next time newb.

 

I am sorry for my n00bness, will do next time. Yes as in I will have to mess around with or yes as in it will work fine?

 

It will work fine. But if you get a converter the speakers will sound better. I myself do not have one, because I am getting a sub anyway. But if you want the full "bose" affect, then you need a converter. Look around in the audio/electronics section for more information on it.

 

i am in the same position as we are speeking
i got a PAC-ROEM-NIS2 which is basicly a plug and play peice for you to just connect the after market CD player to the BOSE amplifier
you can find it on e-bay
i got mine from affsave.com
it costs around $60 with shipping
So good luck