How can I properly paragraph the text of my unpublished short story without butchering story flow and in turn throwing readers off?
I don't understand the question. Do you mean that you've drafted it all as one block of text? Each paragraph should be a self-contained "idea". You should put a paragraph break at a new speaker, or when the narrative moves on in focus.
Read short stories by masters of the form, like Ernest Hemingway, Flannery O'Connor, Alice Munro, Raymond Carver, W. Somerset Maugham, etc. See how the pros do it. There really isn't a better way to learn. If you're writing well to begin with, you should probably be thinking in paragraphs. Don't try to write a huge block of unparagraphed text and then try to put paragraph breaks in. Paragraphs are important tools for organizing the materials of your story to begin with. Think in paragraphs. Let each complete its own thought, and when it's time to move on to the next thought, start a new paragraph. Normally, I don't like to recommend Strunk and White, because I find it fairly remedial, and writers should have mastered what it covers before trying to create works of literary art. But in your case, I do recommend it. It has good things to say about basic paragraphing that would help you a lot, I think.
you should be paragraphing as you write... didn't you do that? short stories are paragraphed the same was as any work of fiction would be...
