I hope this is about the proper window (the one during game setup, not during an empire generation during the game on F9 screen).
"Create one or more computer controlled opponents. These Empires will start in systems Generated by Aurora and they are hidden from the spacemaster." <- This option causes the game to create an x (you enter the number in a window below that option) number of computer controlled opponents at the start of the game. They cannot be interfered with, not even by the space master.
"Generate Empires as NPRs. If this option is in effect, any empires created during system generation will be completely under the control of the program and will not be accessible by the player, even in SM mode. Manually created empires (F9 window) will still be accessible." <- When a new system is generated during the game and a planet fulfilling certain conditions is placed, there is a chance (you specify how high) of an empire being created. If this option is not enabled the empire creation screen will appear, allowing the player to customize it and take control of it. If this option is enabled the empire will be randomly generated and under computer control.
As a side note to all the players seeking help please oh please give as much information as possible, so I don't have to guess, for example, which options are you asking about. The more information you give the higher the chance someone will answer.
