I know the process is a little convoluted. So here is a bit of a walkthrough.
On a new game start the boxes to uncheck are the Computer Controlled NPR, and Real Star Systems. Then change the toggle from starting on earth to "Create Spacemaster Empire". Leave the number of systems at 1000. Change the npr chance to 0. You cana allso change the local system chance to something higher than 50%. This is the chance that when going through a jump point the new system will be within the spread listed just below it. The only drawback of changing this once you get above 75%, you may find yourself being stuck in a pocket universe with no jumps out of a small cluster. I would actually leave it alone for now. Once the game starts you will need to select your "starting race". There will be an entry for SM Race. Also make sure to turn on SM functions.
Next open up the F9 screen (System View) On the bottom right of the screen there are a bunch of buttons, one of them is create system and another is create nebula. They each create a system, with the nebula button creating a nebula system. Create a system, if it does not match what you want delete the system (button on the bottom row). This way you will only have a system in the database that you want. Once you find a system that you like you can create an empire on a planet using the create empire button. If you find a system that you like, but it does not have a habitable planet you can add a colony for the sm empire, open up the F2 screen and choose the enviroment tab. Using a sm only button you can set the gasses in the atmosphere to whatever you want. If you do this remember to delete the colony or it will fix the minerals on the planet. Unless you have played with the minerals this probably means you won't have several of them at all which will quickly kill the game.
At this point you can either start playing the race, or you could decide to create all the local systems using the sm race. I would suggest doing this as the SM race. Whichever race you are going to do this with you will need to change what systems they can access. On the Race Details screen (cntl F2) there are two boxes that are by default 0. The "min Sys Num" and "Max Sys Num". If you enter a system number in these boxes then the race can only find systems in between the two numbers. For a cluster enter something like a 50 system spread centered on the system you created the player race in. You can find them under the Main Information group top left of the screen. Once this is done you can go exploring the local space using the system generationscreen (F9) jump point tab. On the middle left there is a button "enter/explore". If you select a jump point and then click on the button it will take you through to the connecting system. If it has not been created yet it will be at this point. It will take you a while to go through and create all 50 systems this way but it does work fairly well, and doesn't cause to many problems. You will want to make backup copies of the database every few systems in case you mess up at this point. If you do mess up there is a good chance you will corrupt to database and have to start over again. If you want another player race that you control then pick a system and planet that you like and create another empire. A side note, if you want there to be npr's inside the cluster you will need to change the chance on the game info screen. Otherwise wait untill the cluster is done and then change it to whatever you want. At this point also use the sm menu on the main menu bar. There is an option to add extra npr. This will pick a random system and create an npr based on your population when you create them (population of whatever race is the current default race.) If you limited the system number of the player race then you will need to go back into it and reset it to 0 so they can get out of the cluster.
I would suggest that you start by creating a game just to play around with the sm functions on creating systems. It will really help, and should make things much faster overall.
Hope all this helps you, if not ask me specific questions and I will try to answer.
Brian
Hope this helps you out.
