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There is no "correct position" for the nav. Typically then nav in epub3 is a machine parseable replacement for the epub2 NCX plus some extras. It is typically added to the spine with the linear attribute set to "no".
If you want a user TOC and do not want to use the existing nav, then create an xhtml TOC and use that. Then as explained earlier, simply use drag and drop in the BookBrowser window to determine where in the spine it is shown.
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