One of features in Microsoft Dynamics NAV is using of payment discount. You can configure conditions of using this functionality on General Ledger Setup. With this configuration, I mean on Appln. Rounding Precision and Payment Tolerance and types of Payment Accounts from Customer Posting Groups. More about this configuration, you can find using Help for these fields.

We can use payment tolerances and discounts in few different situations. You can see how it generally works on following flowchart:

In my first example, I have configured only payment tolerance without discounts. When we post payment some less from original amount on invoice (e.g. 2.395 instead 2.400), we will get following G/L entries:

If our payment is greater than Invoice Amount reduced by discount, we will get following entries. System will post full payment as original invoice amount plus tolerance and discount, as well:

If payment is less than Invoice Amount reduced by discount, we will get following entries. System will post full payment as original invoice amount, discount and tolerance: