Do I index John’s surname as Jones or do I leave it blank?
It depends on the project instructions or the surname field help (purple circle with question mark). Usually in my batch experiences the field help will indicate to mark it <BLANK> - but I believe I have also seen where it does read 'if husband and wife are listed with one of them including surname ... Include that surname for both.'
So it really just depends on the instructions - but field help should indicate.
From General Indexing Guidelines:
How to Index Individuals Whose Names Were Not Fully Recorded