Custom taxonomies is set using the ‘Post Custom Taxonomies’ settings field, from importing rule settings.
More help on this:
Set the custom taxonomies that will be set for generated posts. The syntax for this field is the following: custom_taxonomy_name1 => custom_taxonomy_value1A, custom_taxonomy_value1B; custom_taxonomy_name2 => custom_taxonomy_value2A, custom_taxonomy_value2B; … . In custom_taxonomy_valueX, you can use shortcodes. Example (without quotes): ‘cats_taxonomy_field => %%item_title%%; tags_taxonomy_field => manualtax2, %%item_title%%’. You can use the following shortcodes: %%item_content%%, %%item_tags%%, %%pinterest_share_button%%, %%twitter_share_button%%, %%google_plus_share_button%%, %%facebook_share_button%%, %%random_sentence%%, %%random_sentence2%%, %%item_title%%, %%item_url%%, %%item_read_more_button%%, %%item_image_URL%%, %%item_excerpt%%, %%item_show_image%%, %%item_show_all_images%%