Backup and restore

ok James - if you go to Moodle on your server or via ftp client you should have a folder Moodle but OUTSIDE of that should be a folder moodledata (or in some installations it is called uploaddata) and that is where all the folders for each course are stored. For example site files that you get to from the front page are in folder/directory number 1. Each course in Moodle has its own numbered folder that gets made once you put something in a course in Moodle. If you have stuff in courses already then there will be folders with numbers - if you go to a course and click on a resource you will see the number in the URL. If you make a new course and want to see its number you can create the folder by just uploading any old thing into it - text file -whatever - and then you will see the number of your course folder. So upload your zipped/backed up course into a folder/directory via ftp and then go to that course and restore it from there. It has worked for me which means your backing up was successful so you didn't do anything wrong.
edit - forgot to say - the moodledata/uploaddata folder *should* be outside of the moodle directory for security - I have never heard of softaculous but I guess it must be like Fantastico?