each multisite will have it's own set of tables in the database. The Atahualpa settings are stored in the wp-options table. This means for each multisite there will be a new wp-options table and a seperate set of settings.
In order to have a customized set of settings, you would have to create a site with the settings you want and then export it and go thru the code and replace the current settings. Note: you would have to repeat this customization each time the theme was updated.
or, you could setup the settings you want, export them and each time you create a new multisite, import the settings into that occurance.
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Juggledad | Forum Moderator/Support