Auto FTP Manager version 5 and newer will run as a service. Create your automated transfer, then schedule it. In the schedule settings make sure to enter a username and password that the schedule will run as. You do not need to be logged in for the scheduled transfer to execute. More information about scheduling a file transfer can be found here: https://www.deskshare.com/help/AFM/ScheduledProfiles.aspx

Using WebCam Monitor in a work environment is legally allowed. Hidden cameras are also allowed when they only record video. A notification on the wall is not required unless you are recording audio. Audio recording in a workplace requires notifications according to Federal or State wiretap guidelines. The exception to video surveillance is where an expectation of privacy is implied - meaning a locker room, bathroom, lounge, break room, etc. Most of the laws were created regarding employers monitoring workplace employees - monitoring for theft is more permissive. Please note that this information is from general Federal guidelines. I don't know of any specific Massachusetts laws prohibiting the recording you are looking to do to catch the thief.