If you have a lot of backups to create turn on Moodles auto backup feature, it will back them up on Cron.
You need to test those backups in a new Moodle, there were some issues with the way they backed up files a while back where the auto backups were not keeping their own copy of all of the files but referencing Moodles repository.
There is something else you need to be aware of if you clone Moodle sites which is any internal links between courses will break.
This is because courses are created with auto incrementing id numbers in the database, the first course created in Moodle is the front page, and each subsequent course increments the ID number accoding to when it was created.
When you import your courses into your new system, unless they are created in exactly the same order, including re-creating and deleting any courses that were deleted in the previous system the id numbers wont match.
So, course id = 123 in the old system may end up being course id = 77 in the new one.
That is not a problem unless you have hard coded links between courses in labels, textual content. If you have then you will find links broken or linking out to the wrong course.
Just something else to be aware of...