You can use envato toolkit WordPress plugin to update the plugin and you can find all information regarding envato market plugin activation and updating themes and plugins via that plugin on the above link.
Or just replace the files to the plugin folder ~/wp-content/plugins/WPShapere/ via ftp.
You have just updated the plugin to the latest version.
Your customized settings won’t affect due to plugin update.
However, it is advised that before updating the plugin, backup all your customization settings from Import-export settings page. And backup database and all your WordPress files so you can revert back in case of any error.