What is the difference between the Arrival & Special Instructions fields?

Arrival Instructions is a pre-defined field where the administrator can add items that appear in the drop down menu.  The operator can choose from the list when pre-registering a visitor.
Special Instructions is a free-form field where the person pre-registering a visitor can specify instructions for the receptionist to see when the visitor arrives.
If there is any data in the Arrival Instructions or Special Instructions fields of a pre-registration, the receptionist will see an "Instructions" pop-up while signing in this person from the Expanded Panel or the entry form.
Both Arrival Instructions and Special Instructions can be added on the email template to the host/secretary and/or visitor. These are available as "Pre Reg: Arrival Instructions" and "Pre Reg: Special Instructions" under Database Objects of email templates.