1) Configure a backup to upload to Amazon S3 (new or legacy version) and use the [SITENAME] parameter in the path (not the bucket).
2) Run the backup from within wordpress and it will upload to the correct location (bucket/[SITENAME]/).
3) Setup a cron job to run (such as "/usr/bin/php5-cli /public_html/wp-content/plugins/akeebabackupwp/app/cli/backup.php --profile=2") and it will upload to a different path, substituting "akeeba-backup" in place of the [SITENAME] parameter (bucket/akeeba-backup/).
Using the [SITENAME] variable was useful for us since we can import an akeeba backup profile and not have to change that particular setting. Is that something that is not supported in the Wordpress version of the plugin?
I attached a log of the cli backup as well as a backup run from the back end.