When you invoice your customer Freight Charges, you should create it as an Income type of account; it will show in your Sales by Customer report as an item sold to the customer.
Although, some user may create Freight Charges as an expense account (usually for reimbursement of expenses incurred), it will still show in your Sales by Customer report.
Example: you invoice your customer Product A for S$1,000.00 with a Freight Charge of $100.00. The double entry for this case will be:
Debiting Accounts Receivable account: $1,100.00
Crediting Sales Income account: $1,000.00
Crediting Freight Charge Expense (In this case, create as an expense account type): $100.00
In order to add Freight Charge into Invoice, you have to create Freight Charge as either an Other Charge item or Service item. Hence, it will show in the Sales by Customer report. This is because the Default Filter for Sales by Customer is ‘All Sales Item’.
If you do not want to show the Freight Charges item in your Sales by Customer report, you can filter your report, you can set the Filter for Account to ‘All Ordinary Income accounts’. Refresh your report; you should see the Freight Charges excluded from your Sales by Customer report.