Need advice - Calibre for converting and managing fanfiction

[valiha]

I need some advice on how to use Calibre to convert and manage my vast fanfiction library. I have tried using this program in the past, installing and uninstalling several times. I cannot stand the fact that it creates a copy of every file I add to it. I understand the reasons for it now though I didn't in the past, but just knowing that it leaves a mess of folders and subfolders and files on my computer drives me batty. It says it is "designed around the concept of the logical book, i.e., a single entry in your library that may correspond to actual e-book files in several formats", but I only keep multiple formats for fanfic, so that seems reduntant to me. I have tried to find answers on the Calibre forum over at MobileRead, but most of the conversations are too technical for me. I hope some of you can at least give me some starting points.

( My issues, let me show you them )