Create separate journal entries for the rounded amounts
Rounding of invoice amount
Goto Accounting -->Settings -->Round Off
Tick the 'Allow rounding of invoice amount' option.
Don't forget to add the Round off Account (Journal entry corresponding to write off amount will be passed to this account)
Goto Accounting –>Customer Invoices -->Create
Here, the 'Total amount' is the actual amount. 'Amount Due' is the amount after rounding off the decimal parts and it is the one customer needs to pay.
Goto Accounting –>Customer Invoices –>Invoice –>Other Info -->Journal Entry
As you can see in the picture a special journal entry is passed to balance the amount.
Goto Accounting –>Journal Items-->Search: 'Round Off'