Payments made against Sales Invoices or Purchase Invoices can be made by clicking on “Make Payment Entry” button on “Submitted” invoices.
Payments can also be made independent of invoices by creating a new Journal Voucher and selecting the type of payment.
For payments from Customers,
Note: Remember to the “Against Sales Invoice” or “Is Advance” as applicable.
For payments to Suppliers,
Note: Remember to the “Against Purchase Invoice” or “Is Advance” as applicable.
If you are receiving payments or making payments via cheques, the bank statements will not accurately match the dates of your entry, this is because the bank usually takes time to “clear” these payments. Also you may have mailed a cheque to your Supplier and it may be a few days before it is received and deposited by the Supplier. In ERPNext you can synchronize your bank statements and your Journal Vouchers using the “Bank Reconciliation” tool.
To use this, go to:
Accounts > Bank Reconciliation
Select your “Bank” Account and enter the dates of your statement. Here you will get all the “Bank Voucher” type entries. In each of the entry on the right most column, update the “Clearance Date” and click on “Update”.
This way you will be able sync your bank statements and entries in the system.
In most cases, apart from retail sales, billing and payment are separate activities. There are several combinations in which these payments are done. These cases apply to both sales and purchases.
ERPNext allows you to manage all these scenarios. All accounting entries (GL Entry) can be made against a Sales Invoice, Purchase Invoice or Journal Vouchers (in special cases, an invoice can be made via a Sales Invoice too).
The total outstanding amount against an invoice is the sum of all the accounting entries that are made “against” (or are linked to) that invoice. This way you can combine or split payments in Journal Vouchers to manage the scenarios.
 In complex scenarios, especially in the capital goods industry, sometimes there is no direct link between payments and invoices. You send invoices to your Customers and your Customer send you block payments or payments based on some schedule that is not linked to your invoices.
In such cases, you can use the Payment to Invoice Matching Tool.
Accounts > Payment Reconciliation
In this tool, you can select an account (your Customer’s account) and click on “Pull Payment Entries” and it will select all un-linked Journal Vouchers and Sales Invoices from that Customer.
To cancel off some payments and invoices, select the Invoices and Journal Vouchers and click on “Reconcile”.