simply fly another constructor into the starbase and choose what it's going to be as a module
Yes, and no. Yes, because this is what it takes to add a module; no, because you can't just choose which module to install. You first have to research the tech that unlocks that module. Some of them are easy to find. There are offensive and defensive modules that have their own branches in the tech trees. Some (the most useful ones IMO) are less obvious. If you want to get more output from your bases, (no matter what type) you'll find that in the industrial branch. To garner more influence via your starbases, research the influence branch.
Some of them are pretty obvious. Some are not. You'll just have to learn the tree of your chosen civ to know what gives you what.
There is a tool to which you can refer that can help you out. It is called the "Galactopedia". You can find it here: WWW Link
It is a little stand alone proggy that will tell you what every item in each tech tree does. Great tool for learning the game.
Hope this has been of some small help. Good luck.