If you configure as described in Using Object Storage for Uploads (S3 & Clones) you should be able to
rake uploads:migrate_to_s3
If you want to stop using s3, then you can enter the rails console and set
SiteSetting.include_s3_uploads_in_backups=true
Then take a backup, make sure that you do not have s3 configured in your app.yml and restore the backup. I think that this will restore backups to local.
But in either case, I would still recommend setting your keys and backup bucket in ENV variables in your app.yml file and then check that you can restore it to a new site.