Not sure if you figured this out yet but here is some help.
Once you have saved the fic to the Doc manager (under publish) you will have to go back to publish and select New Story.
Most likely you will be asked to accept some guidelines so accept those real fast. Once you have done that just select the category for your fic (if it is Naruto you would select Anime/Manga and find Naruto on the list). It will also ask if it is a crossover or not.
From there all that is left is to give the story a title and summary as well as select the language and genre (and a cover image if you wish). Then select the characters involved (usually only the most important to the main plot).
Once you entered that information in you will look towards the bottom where it asks you to select a document (should be one of the files you uploaded to the doc manager). Once you have selected your file you can go ahead and select publish new story.
In the future if you ever want to add on to the story (depending on if it is multiple chapters or a one-shot) you can select "manage stories" under publish to edit existing chapters, the summary, title or even add in some new chapters.
Hope this helped!