The way Jekyll themes — or rather Gem-based themes — work, is they sort of hide all the details of how the site works. You can add or override files, but you can’t really see them. There are benefits and downsides to this approach.
What I think you are experiencing right now is that you cannot see all the minima theme files, making it hard for you to make changes.
Here’s a video I created that might help you understand themes a little better. Specifically, checkout the video staring at 6:24.
In the video, I show you how to view all the files from Minima and make changes. I hope this helps.