How to backup an offsite server?

Yes that is correct

You can use one rclone command to back lots of things up. I'd use the --include-from flag (or maybe the --filter-from flag to set up a list of things you want in and out of the backup, then run rclone from the root of the file system.

So

rclone sync --include-from backup-dirs / remote:backup

For backups, also check out the --backup-dir flag

Probably the most complicated part is the initial setup of the config file. The easiest way is to set up the config file on your local computer then find it with rclone config file and copy it to the remote server.