Alex Scoble cites best practices preventing and pinpointing hacking (or cracking, or whatever more appropriate term we may call such intrusions) attacks on servers. The steps involve setting up adequate logging and auditing, and in the unfortunate event of an attack, analyzing logs and isolating the intrusion. Alex advises not to hide attacks from stakeholders, including your boss!
The worst thing you can do if an attack, or any network issue, is found is to try to hide it. Your bosses will appreciate knowing about problems (or if they don’t perhaps you don’t want them for bosses) and should look to you for solutions versus trying to lay blame.