It doesn’t make any sense to me from the perspective that I’ve approached it.
I think you’ve already identified the issue. Docker is pretty “simple”, but you’ve got to approach it from the right angle or else it doesn’t make sense. Apart from suggesting the official documentation I can’t give you much advice on how to learn it because my path to understanding Docker was pretty much just trying things out and iterating on it. That said here’s a tips that could help:
If you aren’t using Docker Compose already, you really should. Just having your entire configuration for a service in a single file really helps.
Aside from debugging, you normally aren’t meant to run commands manually in a container. It’s best to act like every container is just a black box that simply does its thing.
If you need to edit config files, the easiest way is to just directly on the host if you’re using bind mount volumes, or spin up a temporary container running Debian or Alpine for example that also has the Docker Volume mounted.
As @housepanther has already mentioned, building your own images is also pretty helpful since it strips a lot of the “black magic” away and teaches you how to further “mod” existing images.