When you accept or reject an application and choose to email the applicant, the default address that populates in the "From" field is the shelter's administrative point of contact. The address that sends the email will be firstname.lastname@example.org BUT when the applicant hits reply, their reply will go to the address entered in the From field.
When a user replies to this will be your administrative point of contact (set in Configurations > My Shelter). This article here explains where this information is used: How are Transfer Point of Contact, Administrative Point of Contact, and Permanent Rescue Contact used?
When you choose to email an applicant (when accepting or rejecting their application), you can also change the reply to email by editing the From box in the popup window. The email will be sent from "email@example.com" but if the recipient hits reply, it will be sent to the address you entered here: