The Surcharge was designed to allow taking EXTRA charges in case of credit card payments. For example, if you want to offset credit card processing fees and you want to add 1$ to each booking.
You can add the surcharge in Take Payment window, here:
The surcharge will be visible in Payments tab in Surcharge column:
At the moment a surcharge is added to the reservation it is added also to the reservation Total and the action cannot be revoked. If you edit the transaction, you will be able to edit the total amount of the transaction (the surcharge is included in the amount) but the Total of the reservations and the surcharge will not change.
Check also Collecting credit card surcharge using Coupon option