I wouldnt have it run all the time. The virus threat in linux is EXTREMELY low, and is much lower if you dont run as root and dont execute programs that you dont trust, and of course, dont use P2P.
For having it run on a schedule, you'll want to do some research on setting Cron jobs.
All I have to do is add a script that executes the program in my /etc/cron.daily folder, and the program runs every day at 12:03AM.
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