Mr.
Under the "Deploy" menu, you have the options for "Monitoring Deployment". When you apply one of the templates, you being answered for "to which" device or devices you wants to apply that template, and you can maximize on of that devices and select the interfaces you want to apply it, in the case of that template are interface related (like a threshold or health template). You can choose all the interfaces selecting the device, or one of more interfaces selecting specific interfaces.
Prime infrastructure only will take in count selected interfaces for monitoring and reporting. You can view all interfaces at Device Work Center for those devices.
I hope it helps you, regards.!
Eduardo