If you place stories in more than one category, say both Showcase and Sports, the story will display in both of these sections on the homepage.  The recommend way of working with this is to place a story in the Showcase category first, and then once other stories have displaced it as a top story, change the story to be in Sports category.  This way the story will be filed correctly, but it will not display twice.

Also when placing stories in a subcategory, you do not need to also place them in the parent category.