There are different ways of running SpamAssassin. The method chosen depends on the requirements of the site. Each method has different performance implications and offers different levels of flexibility.
For low-volume sites, Procmail is an ideal choice. It can be used to filter email site-wide, or can be used selectively for users with local accounts. For higher performance, SpamAssassin can be integrated into the MTA.
If desired, email can be rejected upon delivery. This warns a legitimate sender that their email has been filtered. However, if the spam email uses a fake identity or a stolen identity (as is usually the case) the message is bounced back to an innocent user and so this method should be avoided.