Is it the factory fitted cd cahnger your referring to!?? Boot mounted or slave DIN size changer up front beneath or above the host radio??
In either case...if you have a changer connected to your host radio...you can get an interface to eliminate the need for the changer and use the same plug which the changer plugs into for a direct ipod link....brands such as Dension which do the gateway 100 and 200 series fitting and Connects 2 which do the dock cable type fitting. They come in around £85 + from your average audio store available to order otherwise once you establish vehicle model and factory fitted radio type...you can order for a lot less online.
Dension do both dock cable methods (just an ipod plug at the other end routed to where ever preffered like glovebox) and they also do an "active cradle" which you can seat your ipod into to charge and send data through to your radio. The active cradle's require a car specific plastic mount of which you can also order....from a company called "Brodit" and you can go onto their website n put in your vehicle details to bring up photos of your dash and how it would look in the mounting positions available, whether left hand mount, centre or right hand mounts.
A lot of the VW's use the same interfaces as Audi's. So should you go for something made from the company "Connects 2", then you would be looking for sumthing along the lines of part number: CTAADIPOD003
The dension company use part numbers that look like this: GW16AU2 & GW33AU2. (this is also an audi ipod part number)
Audi's do have different radios when on board bose amps are involved though so do check from their websites for vehicle application.
I have read that there are leads out there that you can connect which will allow for you to continue using your changer as normal AND have your ipod running through the same auxiliary input.
The previously mentioned dension and connects 2 methods work in a way where they remove the need for changers and use up the socket in which the changer would normally be using. But the benefit is that your original VW radio is then fooled in thinkin that you stil have a changer connected and enables you to control and change your ipod tracks from your headunit/radio.
There are other solutions that exist in the form of FM transmitters but if you have the ability for a direct interface, I would have thought that it were a more logical approach.
Hope this helps!