All subcontractors have a contact person. That contact person can submit pay applications in order to get paid by the general contractor (i.e. you).
To change the contact person, first make sure that the person is added to the subcontractor company as a contact.
Go to Subcontractors => Contacts. Check if the contact you want to assign the Pay Application submission to is in the list. If not, click "Add a new contact".
To assign a new subcontractor contact who will submit the Pay Applications, open the subcontractor contract. Then click "Change contact person" on top right corner as seen on the image below: