The default webroot location for MODX Cloud instances is at /www/. In addition to the database for each instance, all files inside the webroot directory are included in the automatic nightly backups.
Some application frameworks recommend storing their files outside of webroot. To accomplish this and to have an entire project included in backups, start by first accessing your instance via SFTP or SSH and create a directory on the filesystem inside the ~/www/ directory.
Next, enter this same directory on the bottom of the Web Server tab of the Cloud Edit page. There is a single text input to specify a directory inside www/ that will be used by NGINX as its webroot. Once you save this value, NGINX will then use it as the alternate webroot location.