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One thing I would recommend is installing the product on it's own server and dedicate that server just to EPO.
Here is the link to that pdf file that McAfee helpline referred you to.
Our EPO server, is running on a dedicated server. It is firewalled and has ipsec running which helps protect it from hacker attacks. We only open the ports that are necessary for clients to communcate with. Other ports we restrict via IP ranges so as to protect from outside (internet) attacks.
I'm not aware of a best practices guide for EPO but here is a link that has a master list of EPO 4.0 support articles:
I've found that McAfee is lacking best practices guides for other products as well.
It's also a good idea to backup your EPO database to a flat file wich makes restores much easier.