For how to replace the engine air filter, see 1000q: Passat TDI engine air filter.
1 air filter - this filter was used on many Passat and Audi so you should have no problem finding it at any auto parts store.
Slide the battery terminal cover to the side and remove it. The large plastic piece between the windshield and firewall will come off if you pull it. It's only tucked into the rubber seals around the edges. Note how it sits for installation.
The air filter is visible in the picture above. Just slide it out and install the new one. One area of possible leaks is the gasket between the metal filter housing and the chassis. If you want to do a bit of preventative maintenance, inspect the gasket at the bottom to make sure no water can get in there.
While you're in there, make sure to check for leaves clogging the area behind the firewall and clean as needed. There are a few drain holes where water should drain out. If it doesn't, it can back up into the interior in places like the aforementinoed seal.
Please post a comment in the mk4 VW Passat TDI forums if you have more tips or would like to report broken links or pictures.