Okay so, firt you have to write it up on your computer EG: Notebook, Wordpad etc.
Then you go log into your profile (On fanfiction) and go to Publish: 'Upload document'
You then upload it and go to new story, pick your characters, rating, title etc and upload it on there and either preview, edit or both.
(be sure to edit it just incase)
It could take awhile to appear on the site but it never takes me long so you shoould be alright :D
I think that's how it goes I havn't done it for a little while :)