NT bat file to Perl script conversion

I am trying to take a system that uses BAT files on NT and convert them to Perl Scripts. I am going to run the Perl scripts from Windows scheduler, and I need to know if I schedule them to run as root on the box if the schedule will always be active? Where if it is schedulled as a user it appears that the user has to be logged in. I am not a NT admin and I don’t know if our admins are running schedulled jobs on this box.

I am a long time UNIX/Linux KSH/Perl developer and am trying to convert the bat files to a more standard modular platform.

Any suggestions or insight are appreciated.