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MobiCreator is just a graphical "shell" around the "mobigen" command-line tool. All it does is to provide a nice means of creating or editing an "opf" file; it's the opf file which contains all the "building instructions" - the order of files, the metadata, etc.
If you simply open the opf file from within Mobi Creator (or, in fact, just double click the opf file) everything will be loaded automatically, and you need to nothing more than click the "Build" button to create your book.
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