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You can disable calibre auto-detecting the TOC by typing / in detect chapters in structure detection. Also clicking the Do not add auto detected chapter in Table of content. Normally calibre will use your TOC if it already exists. So I don't understand why you will have double. It is either the setting used or your file has links, which calibre will use if all else fails to generate it.
But you will have to play a while in calibre to fully understand all the settings.
That is why I created my own program to easily edit epub's Table of Content, you should try it, if only to remove duplicate. (Link in my signature)
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