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I have noticed that Atlantis uses smart quotes but this behavior is not documented.
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You can use any type of quotes in your document.
When you type straight quotes (or apostrophes) in a document, the AutoCorrect of Atlantis can automatically replace them with "smart" (or "curly") quotes according to the settings in the "Tools | AutoCorrect Options..." dialog. This feature is well-documented, I think:
http://www.atlantiswordprocessor.com...ct_options.htm
Straight quotes can be replaced with smart quotes not only on-fly (i.e. as-you-type), but also after-you-type. You can run the "Tools | AutoCorrect..." command, and it would suggest various corrections to your document text.
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Also the search and replace functions seem to include some automatic multiple finds such as find " will find regular and smart quotes, find - will find a hyphen, ndash, and mdash. Finding a space will also find variations of spaces such as nbsp. This can sometimes be problematic when doing searching with replacements.
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This is correct. Different types of quotes can look identically under some fonts or font sizes. And quite often, they play the same role in the document. By default, straight quotes are automatically replaced with smart quotes in Atlantis as-you-type. So when searching for text, many users would not need different types of quotes to be reported as different characters. You cannot type a smart quote directly in the "Find what" edit box of the "Find/Replace" dialog of Atlantis (at least there is no simple way to do this). What's more, straight and smart quotes might look identically in that "Find what" edit box. So in many cases it would be counterproductive if Atlantis did not treat all types of quotes as the same character.
You cannot search for straight quotes only through the "Find/Replace" dialog. But if you paste a specific type of smart quote to the "Find what" edit box of the "Find/Replace" dialog, Atlantis would not report straight quotes. If you need to search for straight quotes instead, you can use the "Tools | AutoCorrect..." command of Atlantis.