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If you send your MOBI to the Fire via Amazon's e-mail service it will show up under Docs. If you side-load the MOBI via USB, into either the Books or the Documents folder, it might show up under Books or under Docs. This depends on whether the MOBI has the PDOC metadata tag or not.
For a cover to show up you need a cover entry in the OPF file. How this is specified depends on which tool you use to generate the MOBI.
I find Calibre to be the easiest way to manage ebooks. If you started from HTML or an ePub, you could import this into Calibre and have it convert to MOBI for you (after selecting a cover and getting the metadata right). If you only have a MOBI, import that and do a MOBI to MOBI conversion. Then connect your Fire by USB and Calibre will detect it and give you an opportunity to copy whichever ebooks you want to the Fire. You may want to blank out the "Personal Doc tag" under Preferences -> Output Options -> MOBI, but I have not found this to be necessary.
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