If we use the secondary email field and the unique email constraint is turned on, will this setting also apply to the secondary email field and if so how?
Yes, the unique email constraint will apply to the secondary email field. No constituent record will be allowed to have a secondary email that matches another record's primary email or another record's secondary email. As a result, you can search for a constituent using their secondary email by simply entering the secondary email in the email field when searching.
For information on how this affects constituent matching when a constituent takes an action on your site and is not logged in, please refer to this solution.