Simple, you don’t separate anything because that is going to be terribly complicated. It is advisable to use the standard WordPress import export. See this tutorial:
However, your plugin and theme options will have to be re-set manually after the transfer. If any of those plugins use custom tables, you’d have to figure how the plugin accesses its tables and how is data for that particular blog stored. If everything is custom post types and taxonomies, you are covered.
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