Add NPR from the SpaceMaster menu acts the same as setting the game to generate initial NPR's during game setup.
To create an empire on a specific body, while in SM mode, open up the system information(F9) and select the body you want to use as the new empires homeworld. Then use the create empire button and make sure the create as NPR checkbox is checked, and set the other options as needed.
Note that if you use new species when generating an NPR in this way, it will use the bodies current gravity, oxygen/methane and temperature levels to set the species ideal point. If you want these to be different you will need to create a temporary player controlled colony on the body and use the sm set options on the terraforming tab to set the atmosphere to that which you desire.
You should also probably select the body and use the HW minerals button as well before creating the new empire otherwise the NPR will probably have problems.