Technically, Auto FTP Manager does not run as a windows service. I think your main requirement is to run on a server unattended. Yes, you can schedule Automated Transfer Profiles in Auto FTP Manager to run unattended in the background (minimized to the system tray).
You can create Automation Profiles to schedule transfer the content of folders on a FTP server. If you need to transfer a single file, you can use the following method.
Make sure that the file is created in a separate folder. Then, create a new Automation Profile and specify this folder as the Local or Remote path, depending on whether you want to upload or download the file. You can then schedule this profile to run at a specified time in the background.