Hello,
The reason you see two instances of the "Server" components is to allow you to easily deploy them to an additional subordinate server, since you could have multiple NTA subordinate servers. To deploy a new subordinate you would simply right-click the undeployed component and select Deploy from the subordinate's DMA.
If you don't use more than one NTA server, you can simply ignore the components listed as Undeployed. They are just placeholders for subordinate deployment.