You're right that if you do the RPM install you'll usually get an OTRS
"service" that is responsible for fetching mail from POP and IMAP
boxes, sending out reminders, unlocking tickets and such.
With the manual installation, these are just handled by cron and not a
separate service. So if you're on Debian or Ubuntu, and you'd like to
stop the polling and such because you're doing OTRS maintenance or so,
please just stop the cron service:

sudo service cron stop

if you're done, you should restart cron:

sudo service cron start

Of course you can make a separate service for these cron jobs too, if
you'd wish.