A Planned Gift and its links to realized revenue gift records is not the same as pledges and payments. A Planned Gift does not have a balance. Applying gifts to a planned gift as realized revenue does not "reduce" a balance/amount on the planned gift.

For example, we were notified of a planned gift from Clara Daniels on 9/14/15 for $500 to be received from a Bequest:
planned gift record

However, when the funds for the Bequest were received, we received a Stock/Property gift for $750 of Blackbaud stock:
stock/property gift

Applying this gift to the planned gift lists it on the Realized Revenue tab of the planned gift record:
realized revenue tab

As far as The Raiser's Edge is concerned, it's "okay" if there is a difference between the Gift Amount and Total Realized. However, please consult with your financial area or other accounting resources to address any questions and the appropriate policies/procedures should the amounts need to balance for your organization's unique financial records. If the amounts need to be the same, edit the Gift Amount to match the Total Realized.