If you sort transactions by payment method

Deposit adjustments entered in the Bank & Deposit Adjustments window will display in the Prepare Bank Deposit window only when All Methods is selected in the Select Receipts by field.

If you select a payment method other than All Methods in the Select Receipts by field, deposit adjustments won't display in the window, although the amount will be included in the Prepare Bank Deposit transaction.

When you record a deposit adjustment, the adjustment is marked automatically to be included in the Prepare Bank Deposit transaction. So, no matter how your transactions are sorted, if the deposit adjustment is marked for deposit, it will be included in the deposit transaction. You'll see the amount reflected in the Total Deposit Amount field.