I do everything manually (use the suggest setting, just to get reminders). Let me give you a "get set up" strategy, for once you start a new game:
1) Pause the game.
2) Go to you ship design screen, click "all non-obsolete designs". Sort on role. You may now change any of the designs you have. It is not necessary, but you may not want your destroyers to have troop carrying capacity, you may want you military ships to have more fuel storage, etc. Take your time, the game is on pause, lol.
3) Go to your research screen. In each tab, click what you would like to research. Develop a plan, like I will be using fighters, but not missiles. Research accordiingly.
4) I then use the left quick find lists to stop every Constructor, Explorer and every military ship of frigate or larger, and take them off auto. I let escorts stay on auto.
5) Run the game for one second. This will update orders. Constructors will now show on your expansion planner. Set them to build mines and gas extractors according to your empire priority. Set explorers to go explore nearby unexplored systems. Get you military (frigates and larger) into one fleets. Assign an admiral.
6) Thats it, your on your own now, kid, lol.