I think Calibre is a great program but I have to agree that its really annoying that you can't choose the output file structure. Whilst it is an excellent idea to structure it by Author, the problems arise for me when I have a lot of textbook ebooks and have no idea who the authors are as I can identify them better by category. I just use a different folder then copy them across into folder I wish to use, annoying but such is life
I Cant be lazy all the time lol!