Help with formatting

[sheepsclothing.livejournal.com]

 Help! 
So, I did buy the Sony 600 after reading everyone's comments...thank you so much! I'm getting used to the fact that the screen doesn't glow like my Touch, and I did buy the cover with light so I could read in bed. 
Anyhoo, I don't really feel like I know what I'm doing. Some fic has been downloaded, and I've had no problem using Calibre to 'auto convert' it to my 600. Other fic hasn't been so lucky! I thought I did it right only to find on climbing into bed, that there was no content.
Today, I was trying to convert 'Absolution by wolfling and omphalos and Calibre couldn't or wouldn't do it. The authors kindly saved it as one file so we wouldn't have to go searching for a million chapters. Yesterday, I saved it as an html file, and Calibre didn't like this. Today, I downloaded it again as a text file, and it seemed to go Ok, but didn't convert. The other options were pdf or doc. 
I have RTFM but it isn't much help. I really need a step by step tutorial, you know, 1. do this 2. then do this! 
I also want to sort my SPN fic into some kind of order, so I can find it again. Can't we make folders or anything? What about multi chapters? I'm taking the thing to a slash get together this Saturday, and I'm going to be so embaressed if I have this unholy pile of crap on the Sony with no organization at all. LOL!