Under Application Management, you have ‘Manage Service Applications‘. Here, you actually manage the different properties of the services themselves. For instance, when clicking on the Managed Metadata Service, you are directed to the Term Store itself, where you can create or add to an existing Taxonomy Term Store.

The other one is under System Settings. That one is ‘Manage Services on Server‘. Here, you will find a list of all the Services installed on the server, along with the status of each (whether it’s stopped or started). Another column gives you an action to accomplish. If the service is stopped, you can start it, etc.

If you are starting out, and somewhat confused concerning the functionality of the two items, this should help you out a little.