Hi Anh,
Apologies, I realise my question was not well written.
The taxonomies are not already setup, they are imported directly into a fresh WordPress database using SQL - these scripts form the WordPress taxonomy hierarchy by creating entries in wp_term_taxonomy that relate to the imported wp_terms data.
At present, the scripts also add related taxonomy meta into wp_termmeta, although I wish to use Metabox's Custom Tables feature to store these entries in a separate table.
Maybe this is straightforward, so I will give it a try and come back if there are any problems.
Thanks,
David