Yes, but the method for doing this I am generally not a fan of. (Journal entry)
I'd be tempted to instead do the following:
1) Record the unkown payment on the make deposit page using "other deposits" to an account called "Unknown customer Payments" (or some other name)
2) When customer is known, record customer payment for correct amount - with the other side in undeposited funds.
3) Use the make deposits screen and deposit the customer payment, but use the cash back subtab to record to the "Unknown customer payments" account.
adds an additional step, but removes a brittle application step from the cash application process