Can i have a extra cd player installed so i can have the navigation disk in it and still be able to have my audio/dvd in the main HU?

Or will this not work?

I can't see how this would work, simply based on the idea that the Nav Disc wouldn't work if you stuck it in a home dvd player.

Even though its DVD based its not necessarily designed for any dvd drive.

It will only recognize the main drive as the source for nav data. Your only recourse would be to either install a CD or DVD changer or ipod and use that as your main media source.