You have to use the VW SD card a new one will not work on the vehicle. You take it out, put into pc/laptop and then copy everything to a folder to use as a backup. Then format the card, once that is done extract the new data onto the card and insert back into slot 2. Once the ignition is on the data can take a couple of minutes to register and then you are good to go.
The update is only the maps, if you are having problems it is worth taking to a dealer as they are the only ones that can do the firmware update. Some have had similar problems and the update has fixed it. They usually put the latest maps on at the same time.