Updating the component

The 'correct' way is to uninstall both and reinstall. However, updating via FTP should be fine as well. The Component does not uninstall it's database when you uninstall, so you won't loose any of your config settings. The Module will loose it's settings when you uninstall. FTP'ing the new files for the module would prevent the loss of settings, but you should open the module and hit 'apply' or 'save' after you update to make sure all the parameters are correctly saved (again).

The configuration data is stored in the database and never deleted (even if you uninstall). Not sure what issue you're having, but you should definitely be able to uninstall JFBConnect and then reinstall it like it was new. All your old settings will remain. The only caveat to this is if you changed the template files, without creating template overrides.

I wouldn't recommend manually copying the files, as we make database changes in the installer script (to make your configuration names use the most recent name) and install the newest version of some plugins and the login module in the process.

Hope this helps, but again, if you're having issues, let us know what it is and we'll help you overcome it in the best possible way!