At the bottom of both automated and custom emails/alerts, you will find a link to unsubscribe. If you follow the link from an automated email, it will unsubscribe you from just automated emails. If you follow the link from a custom email, it will unsubscribe you from just custom emails. 

Alternatively, when a user logs in to their user account, they can unsubscribe from 'Alerts' and 'Career Center emails' (separately) under Alerts & Emails.