Phase 1 of the Operations Manager 2007 Security Guide is now available online at http://www.microsoft.com/technet/opsmgr/2007/library/proddocs.mspx
The first phase of the Security Guide was written rather quickly to address the top two security-related concerns that we received; information about accounts and how to use certificates. In addition, the MOMCertImport tool was improved before we shipped Operations Manager 2007, the MOMCertImport tool can now import certificates directly from the certificate store. No longer do you need to export certificates into a .pfx format before importing them into Operations Manager 2007. Phase 1 of the Security Guide contains the how-to topics using this feature of the MOMCertImport tool.
The command to import a certificate directly from the certificate store is:
MOMCertImport /SubjectName <Certificate Subject Name>
We are currently working on Phase 2 of the Security Guide; expect this to be available near the end of June or early July.