zaccaria,
The Navionics card does not determine how many waypoints you can have. The 797c will handle up to 3,000 waypoints with its internal memory.
You would want to export the Nav data to another SD card to transfer to other units or to the computer.
I would not recommend saving anything to the Navionics card. You can damage the Navionics card if you save anything to it and corrupt the file structure.
Hope that helps,
Robert