The game is pretty complicated, i agree, ultimately though, there is a bit of a sandbox vibe to it.
Making mistakes doesnt mean you have to start over again, you could just keep going and try to fix mistakes in progress.
As to the thing with star bases, there are, in the base game, 4 basic uses for starbases.
1) ship construction centers, which you would want to have shipyards, crewquarters, and fleet academy.
2) trade hubs, which collect trade resources, with a range based on number of trade modules, which you can upgrade with offworld trading company for a free trade bonus, you need these to collect silver rings, which is the icon for trade
3) bastions, which use guns/missles/hanger bays to do 2 things, protect choke points from alien attacks and prevent piracy. If you toggle the trade view map mode, the 2 arrow icon bottom right, where you see red skulls, you need to put a bastion nearby. The protection range of bastion is equal to number of combat modules, so 2,4, or 6. Hangers provide more anti pirate value but are weaker against enemy ai. Need to research strike craft to unlock hangers.
4) Naval outposts, increase your naval capacity, each naval outpost module gives 4 points of naval capacity, can be placed anywhere, but I tend to put them over inhabited planets since exact placement doesnt matter. Can be upgraded with naval logistics office to provide 6 naval capacity per module.