The following are my opinions.... Headers & footers take up too much space on a page and look ugly. Line spaces between paragraphs to seperate paragraphs also are ugly.
Now I am done with opinions. Onto facts that need to be said...
Book Designer has a serious bug in it when it comes to loading text files. When loading text files, BD can mangle the paragraphs. It does not do this when loading HTML or RTF. So if you have a text file to load, use a program such as Word to save it as RTF and load that. But if you have a choice from PG to load text or HTML, always go with HTML.
Next problem is that there is no mention of using Book Cleaner. Without a properly setup Book Cleaner, you will possible have errors in your eBook that you would not otherwise. There is a thread on MR with proper Book Cleaner configuration files and instructions on how to set it up.
Lastly, in the Make Sony Reader file options screen shot, you have two options set incorrectly in misc. toc should be set to full or all and not short. If you have it set to short, you can find missing ToC elements sometimes. Also, dashes should be set to as it is and not short. But setting them to short, you lose any em or en dashes on output.
I personally have nothing checked in book elements or headers/footers. I find that makes a much nicer looking eBook.
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