1. Go to the Accounts module
2. Click on Sales Invoice
3. Open the Sales Invoice against which the payment is received
If there is any outstanding against this invoice a "Make Payment Entry" button will appear. Click on this button to proceed.
This will open a Voucher to make the payment entry. The default voucher type is "Bank Voucher". Select this to accept a cheque payment.
Scroll below to enter the bank account and amount details.
Now you can Save the payment entry. On saving a voucher no is generated.
The voucher can still be edited after saving. On saving a "Submit" button will appear. Once the voucher is submitted the accounting ledger entries will be affected. This will also update the outstanding amount in the corresponding "Sales Invoice"
Hope this helps to accept Payment against a Sales Invoice in ERPNext.
To register for free trial visit http://www.erpnext.com