In english class, they taught me what a clause was, and the difference between an independent and a dependent clause, and how to use a comma with all grammatical correctness to separate them.
But that’s not how I learned how to use commas. If you took most of my sentences and asked me to explain why a comma belongs here or there, I would have to tell you half the time that, grammatically, I have no frelling idea. It just feels right.
See, I learned to use punctuation, not from english class, but from reading. I read a lot. I learned these things organically, from seeing them used properly, a million times over in hundreds of books over the years. I use commas and such by feel, much like a musician might know how to play from sheet music, but still be able to listen to a song and play it by ear without the music written on paper.
It can be hard to describe sometimes, especially when I tend to be such an analytical person. A comma, to me, doesn’t represent a grammatical technicality, it’s a pause for breath. A semicolon is a longer pause to collect your thoughts while linking two ideas. An em-dash at the end of a piece of dialogue means the speaker was interrupted, and an ellipsis means they trailed off. When writing fiction, grammar isn’t important. You can write run on sentences if the narrator’s voice calls for it – incomplete sentences even.
What matters most is the effect what you write has on the reader. I think the only way to gain that intuitive sense for what effect any particular punctuation and sentence structure is going to have is the organic way – by reading extensively, and watching the masters do it.