The key to upgrading MODX is backup & testing. It is imperative test all features after a major system upgrade, because some packages can break. Before upgrading packages or systems, look for upgrade notes within the website's wiki page or client's job notes if no wiki exists. Also, before upgrading ensure there is enough room on the server for at least double the current file size.
Either using the Manager or SSH update / create an .htaccess file behind the manager folder with the following command:
order deny,allow deny from all allow from YOUR-IP-ADDRESS