NightWing, do you have a word processing program? I don't know if this helps you, but to upload my stories, I first type in my WP program (in this case, AppleWorks on a Mac) complete with whatever special formatting I want (bold, italics, etc.) and save it as a normal file. Then, I save it a second time as an html file. When I go to upload, I open the html file on my computer (all the tags/codes are there) and copy & paste it in the AFF text field. So far, this method has worked great for me.
I'm guessing you use a PC running windows; I'm a PC/Microsoft idiot, so I don't know if the same thing will work for you.