The Alien Automator is pretty easy to use and there's not really much you need to do. But it is essential to read the full solitaire rules and experiment with the programme first before playing a real game.
1) When the game starts, choose your level: Easy, Normal, Hard, Harder, Really Tough, or Good Luck!
2) When a new economic phase starts, click "New Economic Phase"
3) New unrevealed fleets might appear on the bottom left. They are fleet symbols with a number on the top right that represents which number fleet it is, and a small number in white saying how many CP it contains. These fleets are not yet revealed (remember, you only calculate what is in the fleet when you fight it). When these appear you should launch them on your game map, but don't click on them yet.
4) When alien fleets engage yours, now click the "unrevealed fleet" and "reveal" them. The content of the fleet then appears in the tab in the centre.
5) When alien fleets see your tech, make sure you mark this in the checkboxes immediately. (Otherwise the alien tech purchases will be wrong)
6) When alien fleets buy tech, it appears in the messages at the top, and on the tech pane for that alien. Click on the different tabs to see what techs each alien has.
7) If you attack an alien home world it needs to build a defense fleet. Click "Build Defense" - using the button of the right color. Use the Homeworlds at the top right as tabs.
That's it!
You also have a log on the bottom right of everything that has happened, including die rolls for the alien players. If something strange seems to be happening, check there to see what happened. To save this log in a file click "save log file" (at the top left)