Handle to hidden command line activity

I am using a script dialog to make a command line backup process (Acronis Backup Advanced) automated. I am working with techniques like this one where you showed a way to read data in from command lines. It is working really good. However, if a backup is going to take 30 minutes I don't have a way to stop it once the window is hidden. I am looking into some option to do this in Acronis' command line option, but I would like to know more about this for other command line projects because I have fallen in love with doing things this way. Thanks