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All books are supposed to be in the Documents folder. That's why there's only one option.
As for the other problems, you'll find that formatting varies between ebooks. If the book is DRM-free you can do a mobi-to-mobi conversion in calibre and select the option to add a space between paragraphs if you wish. The ?, # or other random characters are a sign that someone didn't edit the book properly for conversion issues, or there's some encoding in the file that's not compatible.
The difference in text darkness is something I've only encountered in PDF files, but I wonder if Topaz might have this issue as well. I don't know much about Topaz because when I inadvertently end up with one, I convert it as soon as possible.
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