Using the Application for Employment (if requesting the reference name and email address) as my example you would need to go to the Questionnaires Actions link here and choose "Add Action":
There you will need to add the references name & email fields as well as the email template (see note below regarding email template) you would like sent to them:
NOTE - When creating the email template in your library, make sure to include some text of what the referral needs to do as well as include the merge code for the reference check questionnaire.
You can also decide if you would like the references to go out upon submission or at a later stage (such as Reference Check). If you decide to have it go out at a later stage you will need to edit the Stage via
Setup--> Configure --> Configure Application Workflow Stages and set the questionnaire action within the stage. Please note that you must set the Questionnaire actions first prior to this step.