what hot fixes do you have installed for msme?
you should at least have patch1 rollup2 and hf 904321installed.
if you want to just scan emails inbound then you can do this by going into the msme gui and click on settings & diagnostics
this will show the on-access settings page in the center frame. under microsoft virus scanning uncheck the enabled box
under transport scan settings uncheck scan internal and scan outbound emails
click apply to save the settings
If the McAfee ePO Agent is installed locally on the Exchange Server then it will recognize the fact that MSME is installed.
Policies will depend if you have the MSME Product Extension installed in ePO and that Policy for MSME is set to "enabled".
If so then then anything you configure locally will get written over at policy enforcement time - so should be configured in ePO side.