You can enter pre- and post-session SQL commands on the Properties tab of the target instance in a mapping. You might want to run pre- and post-session SQL on the target to drop indexes before a session runs, and recreate them when the session completes.
The Integration Service runs pre-session SQL commands against the target database before it reads the source. It runs post-session SQL commands against the target database after it writes to the target.
You can override the SQL commands on the Mappings tab of the session properties. You can also configure the Integration Service to stop or continue when it encounters errors executing pre- or post-session SQL commands.