For Trusted Application and IPS Rules, you should always have the McAfee Default policy assigned, as well as a custom policy, so you can make changes to the default policy. Both policies are then rolled up into an Effective policy.
See page 38 of: PD22894 - Host Intrusion Prevention 8.0 for ePO 4.5 Product Guide
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Hi just found the following in the Help of EPO
Assigning one or more instances of the policy to a group or system in the ePolicy Orchestrator System Tree provides for single policy multi-purpose protection.
The IPS Rules policy and the Trusted Applications policy are multiple-instance policies that can have more than one instance assigned. A multiple-instance policy can be useful for an IIS Server, for example, where you might apply a general default policy, a server policy, and an IIS policy, the latter two configured to specifically target systems running as IIS servers. When assigning multiple instances, you are assigning a union of all the elements in each instance of the policy.Note: The McAfee Default policy for both IPS Rules and Trusted Applications are updated when content is update. McAfee recommends that these two policies always be applied to make sure protection as up to date as possible.
For the policies that have multiple instances, an Effective Policy link appears to provide a view of the details of the combined policy instances.
This is realy clever indeed.