"Can I run Complete Cleanup in the background and do automatic cleanups?"

Yes, you can run this software unattended in the background. To do this, simply click the "CC Settings" button, then select "Auto Cleanup" to select your cleanups, and how often you want the cleanup to take place. (This feature is not available on the trial version).
Once you click "Ok", the software will disappear and become minimized in the corner of your screen, and the cleanups will all happen automatically without user input. To stop the automatic cleaning, simply click the box and Complete Cleanup will pop open for you so you can close it, or perform any additional cleanups.