Hi again.
I am sorry to say that there is a limit on what help I can provide as support, but I will try to help where I can.
In your first post you said:
I have my own custom theme with custom queries.
The custom query might look like the ones in this Codex page:
https://codex.wordpress.org/Class_Reference/WP_Query
Scroll down to the sub title Simple Taxonomy Query.
You see how, in those various examples, they pass arguments to the query, in elements like this:
'relation' => 'AND',
In order to attach our filter to that query, you can add an extra argument at the end, like this:
'search_filter_id' => 123,
Where 123 is the ID number of the search form.