That last topic is what I'm struggling with finding info on right now. A search of the term 'NPR" has 0 results on the tutorial and academy boards.
Unfortunately, this is going to be quite short.
Setting up an NPR that you end up running yourself is done exactly like setting up a player race - in fact, it really is setting up a second player race. That's not a bad thing, as by restricting oneself to the currently-selected race's view, maps, and events window you gain a completely different perspective on things, as ships, star systems, planets, alien races, etc. are all referred to by the viewing race's chosen names. It's quite possible to encounter the other Player Race's ships and not realize you're playing two sides of the same conflict at the same time.
Setting up an NPR that the computer is going to run is done almost exactly the same as setting up a player race - at first. The initial race selection screen allows you to choose the empire name, government type, species,species name,empire theme, commander theme, homeworld name, conventional vs TN, etc. settings for the race, after which you check the 'Create as computer-controlled empire (NPR)' checkbox and hit the 'Create Empire' button. At this point, the computer takes over and you're done. The downside is you never get to 'run' the race, and it won't end up exactly the way you want it.
Taking an already set-up race and placing it under computer control is not possible at the moment - too much of the code that actually runs the NPR AI would break - but it's on Steve's list for future development. Turning an existing NPR into a player race can be done, but it's a one-way conversion. Still, it's a nice way to represent an alliance that has become so firm it's practically one polity. (Or for the more bloody-minded, a conquest so thoroughly subjugated that they are now and forever more will be an enslaved part of your Empire.)