Setting User field type from a front end form
Maybe I don't quite get your problem, but I actually don't see any difference between posting child entries (the patients) related to a parent user and posting questionair entries related to a child entry.

You need a hidden field like this for the child registristration.

{% parentId = entry.authorId %}
...
&lt;input type="hidden" name="fields[parentUsersField][]" value="{{ parentId }}"&gt;


You can now link to the child entry and allow the parent to enter the questionair form.

{% set childId = entry.id %}
...
&lt;input type="hidden" name="fields[childEntriesField][]" value="{{ childId }}"&gt;


Keep in mind that relation fields can hold multiple elements, even if set a limit in the field settings; so you need to post an array using the syntax show above. There's other more  complete code examples here on Stack Exchange for having relational fields in a from (i.e. "Creating comments via a related section").

And yes, using a channel for the questionairs is a very flexible and clean way to structure the relation in my opinion.