From the replies it sounds like I am an old fashioned girl, I save all the parts of a story (unless I get it in stages, like time stamps etc) in a word doc, convert that to RTF then load the RTF into Calibre,from that I create a mobi or ePub as required. This way i have the story on my PC in word as well as the ebook, it gives me the greatest control.

If I have a load of small stories by one author then I might save the as one document, but generally its one story one word doc. I then use the cover generate plugin in to create ebook covers