Upon checking, this is covered in the enhancement request logged on Enhancement # 102645 Transactions > Accept Customer Payment : Ability to expense a bank fee on the customer payment screen. You can go to SuiteIdeas page to vote for the enhancement.
Apologies for the inconvenience this limitation may be causing you but I hope this helps clarify your concern.
According to the Enhancement details, below are the three options you may consider as a workaround:
Option 1. Use Bank Deposit
a. Invoice GL Impact
Debit: Accounts Receivable 100.00
Credit: Sales 100.00
b. Payment GL Impact
Debit: Undeposited Funds 100.00
Credit: Accounts Receivable 100.00
c. Transactions > Bank > Make Deposit.
— Use Cash Back Subtab.
— Enter the Account and the Amount.
— Mark the Payment for Deposit.
— Deposit GL Impact:
Debit: Cash 80.00
Debit: Bank Charges 20.00
Credit: Undeposited Funds 100.00
Option 2. Use Journal Entry
a. Transactions > Financial > Enter Journal Entries.
— Journal Entry GL Impact:
Debit: Bank Charges 20.00
Credit: Cash 20.00
b. On the Invoice > Click Accept Payment.
— Select Invoice.
— Enter Full Amount.
— Payment GL Impact:
Debit: Cash 100.00
Credit: Accounts Receivable 100.00
Option 3. Enter the charge during reconciliation
1. Go to Transactions > Reconcile Bank Statement. Click the Other Charge tab.
2. Enter the fee information, and click Add. Once you have reconciled your bank statement, click Save.