priority of hide fields

I have a form with multiple fields.

All the fields apart from the first are hidden through the advanced options for that field, i.e. will not appear on the form.

the first field is a question asking for a 'yes' or 'no' answer through a single choice property

if the answer is yes then then a field asking for a unique identifier appears, this is set in the Options and is verified through a spreadsheet lookup. But all remaining fields are appearing.

Do I have to set each of the fields in the form options to be hidden as well?

I want only specific fields to appear as the form is filled

We are not sure what exactly are you looking for, please elaborate more on this request.

Well simply options are appearing where they are being told not to. What has priority the advance option in an element or the form option?

Currently, you are using a conditional logic to hide all the fields if the question 1 is empty. Which means as soon as users select an answer for it, all the fields will populate

You need to take slightly different approach if you want to enable fields based on users answer.

First, hide all the fields except the first one. How to fields in JotForm

Then add conditional logic against the questions which you want your users to fill in order for other fields to appear. Refer to How-to-Show-or-Hide-Fields-Base-on-User-s-Answer

E.g If Question 1 is filled then Show Question 2. In this case only the Question 2 will appear as soon as the Question 1 is answered, rest all will still remain hidden. 

So on, you have to add multiple conditions to achieve what you need. 

Let us know if you need further help.