You need to separate out groups, branches or parent/child tags into separate custom taxonomies. In the case of your form, this means you plan to category twice. In general, you can use a particular Taxonomy, such as Category, (or Tags, each Taxonomy and each Custom Field) only once in the form. This post tries to explain this a bit better (you can use a plugin to switch category terms from category to any new taxonomy that you make, so it is not so hard to do). It is a really awful preachy lecture I wrote:
https://support.searchandfilter.com/forums/topic/multiple-categories-combination/#post-55166
Sorry about the tone, but the message is right and it links to good plugins (except taxonomy switcher I think).
Taxonomy switcher is a ‘use once and remove’ type of plugin, and it uses ‘hidden’ features in WordPress that have not changed for about 2 years.
Let us say that you have Categories (as WordPress calls them) on some posts, and some of them are fruit types. For example, Apple. Now you decide to have a separate taxonomy called Fruit Type. You may have hundreds of posts with those fruit types already in Categories, and don’t want to retype them all again. Let us say the the Apple ‘term’ has an ID # of 234 (they all have ID numbers). You tell Taxonomy Switcher to move the term 234 from Categories to Fruit Types, and it does all the work for you. You can do a whole bunch of IDs at once, all you need is their ID numbers.
IF you went in to one of our forms in admin, to the Tags, Categories & Taxonomies settings tab, find the line for Categories (in this case) and use the search to ‘add’ all the ones you want to move, then you will see in the settings box all the ID numbers you need to be able to do this. So, cut them from that box and paste them in to Taxonomy Switcher.
Be wary if you have child terms though (those which have a parent), as the parent may have to be moved also.
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