Is there a program where I can write and design story layouts?
I don’t know of any program designed specifically to do this. When I do writing, I usually do it in OpenOffice, and save it in HTML format, but then I’m usually going for a fairly simple, web-presentable layout rather than something fancy. I’d say that for the most part, getting nice layouts is more a matter of learning how to use fairly versatile programs properly rather than getting specially tailored programs. If you’re just keeping the stories on your hard drive, then Microsoft Word and DOC format are probably your best bets, on the other hand if you want to put them up as web pages on the Internet then OpenOffice and HTML formats are probably better.