Checking Account GL Payments on Bank Reconciliation
If you need to record income to a bank account and have it show on the bank reconciliation without linking the payment to a specific customer account, create a journal entry by going to Ledger -> Journal Entries -> New Journal Entry.
Select the bank GL account for one of the lines on the journal entry.
You can then proceed one of two ways:
1) Create a bank deposit for the payment (Income -> Bank Deposits -> New Bank Deposit), include the payment in the bank deposit (General Ledger Entries section), and then mark off the bank deposit in the Deposits Pending section of the bank reconciliation (Ledger -> Bank Reconciliation).
2) Directly mark off the payment on the bank reconciliation (Ledger -> Bank Reconciliation) in the Direct GL Receipt Entries section.