Usually there is no problem retaining your workspace and bookmarks when you upgrade or uninstall/reinstall Notes. But if you're concerned, you can copy the following files before upgrading or uninstalling/reinstalling, and then add those files back in afterwards.
In the .../Notes/Data folder, copy the following files:
desktop8.ndk (may be desktop6.ndk, depending on your version)
If you want to save a copy of your Contacts as well, you can also copy:
For more information on which files to back up when upgrading, see: http://www-10.lotus.com/ldd/dominowiki.nsf/dx/Backing_up_and_restoring_Notes_client_data