Hallelujah, you've seen the light. Welcome, brother
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You're right, though. If you try and "fight" BD it's a lost cause; you have to set it up the way you want it and then just let it do its own thing.
My basic procedure is:
1. Load the book.
2. Select "Tools/Element Browser" and find all the titles. If there's anything that shouldn't be a title (BD is a bit keen on changing any single word on a line into a title!), change it back to "Paragraph". It's the "Title" styles that end up in the TOC.
3. If the book doesn't have one, add a nice cover page and table of contents (I like to have a table of contents at the start of the actual text, as well as the Reader TOC).
4. Make sure BD has gone the styles right for the author and title (it more than not gets them back to front - there's a button to swap them around)
4. Generate the book.
My standard settings are:
Language: German (this gets you all the accented characters - if you use English, they get changed to Russian characters!).
Page margins: 10px all round
Book elements: Author from last name
Headers/Footers: Header off, footer on
Skip cover page and title page (I prefer to do my own)
Page breaks: on
User page breaks: on