00 vw passat wiring diagram troubles

If the harnesses are different, then they probably won't integrate with eachother.  Sometime scars with the premium sound systems from the factory are really hard to work with.  Often times the headunit you see is actually a pre-amp that feeds a factory amp.  The speaker wires and things come of off that amp, and the amp won't recognize an aftermarket head unit.  In other words, you have to wire around the amp to make it work.  I know you said that your car has a Panasonic deck in it now.  If the plugs you see when you pull the deck out don't match the new deck you bought, try gently pulling on the harness to see if there is a second harness hidden down lower in the wiring.  I ran into that in Toyotas with the premium systems in them. 

These were all best case scenarios.  Logically I would say that the deck you bought simply won't work and you need to find a deck with the correct plugs.  I could be wrong, I am not the authority on German cars, and maybe some of the pros in the forum could help you better.  Just out of curiosity, why don't you just get a new aftermarket deck?  It will sound better if you ever upgrade the system than a factory deck ever would.