Your description suggests you're using IEEE 2006 referencing. Had you created them using Word's referencing tools, the sequencing for both the citations and bibliography would have been automatic. Doing the job manually basically requires the use of a bookmarked SEQ field for each 'first' citation of a work in the body, then cross-references to that for each subsequent citation and the bibliography. That way, insertions/deletions of citations can auto re-number. If you then use a table for the bibliography, Word's table sorting tools can then be used to sort the references.

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Cheers,
Paul Edstein
[Fmr MS MVP - Word]