We are tuning our OSSEC server/agent environment. 
We have multiple environments and use Puppet for configuration management 
and AWS for our cloud based systems. 

We baseline (run OSSEC) at the start of an environment build, and then do a 
Puppet apply. 
We seem to have thousands of alerts coming in (many to do with syscheck on 
subsequent Puppet applys). 

How do you guys deal with so many alerts - do you try and whitelist all of 
them in the local_rules.xml file or just let them all go in to the alerts 
file?
How do you know if an intruder has compromised a system if you constantly 
have login sessions opened and closed by system users and have level 7 
syscheck alerts by Puppet applys happening as part of the normal running of 
your environment?
How do you have warning systems based on alerts set-up (e.g. a script that 
triggers to Nagios ? or something else?).

Cheers

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