If you buy the full US/Canada version then you can update throughout that area for a period of one year (subscription period). At the end of the period, you can renew and continue to update or you simply keep what you have updated up to that point.
When updating, you drag a box to encompass the area that you want to download/update. Make the box as big or small as you like. Bigger is longer download times and will also fill the 16gig card faster.
What is on the webapp is what is available. If you see rivers on the webapp with detail you want, it is probably sonar charts, which is information added by users and added to the download database. If there is a list of lakes on the website, that is probably what Navionics has previously mapped themselves (my guess on that topic).