Hello Emily Proctor,
Hope you are well. Thanks for writing to us.
For custom taxonomies WPDM has its custom categories and tags. For more custom fields you can check this add-on, https://www.wpdownloadmanager.com/download/advanced-custom-fields/
You can use categories, tags or custom fields on Bulk Import csv file, you can also overwrite existing fields using ID column, you can use this CSV file for your purposes, https://www.wpdownloadmanager.com/wp-content/uploads/2020/06/sample.csv
For filter hierarchy, you can checxk this add-on,https://www.wpdownloadmanager.com/download/wpdm-directory-add-on/ and these shortcodes, https://www.wpdownloadmanager.com/doc/short-codes/
Please kindly check and let me know.
Thank you and regards