How do you allocate a Customer's payment for invoices during May, when they took a 2.5% settlement discount at the end of June? I need to send their statment for June

Glad to have you here and be able to help you out with your concern, erlo.

Let me share some details on how to allocate your customer's payment for the invoice in the previous month.

We'll need to open the invoice to assign the 2.5% settlement discount in June. The steps below will walk you through the process. Here's how:
 

1. Go to the +New button.
2. Click Invoice under Customers.
3. In the upper-left corner, click the Clock icon.
4. Hit View More to see all invoices you've created before. We can customize the dates by clicking the Date Filter drop-down arrow and then click the Apply button to find the invoice easily. 

Then, make sure the amount received is the same as the original amount to zero out the balance. The original amount is calculated with the added discount. Then, Save and Close. For additional reference, here are the sample screenshots:

Once done, create a statement for your customer. Here's how:

1. Go to Sales on the left panel.
2. Select the Customers tab and find the customer name.
3. Next to the Create Invoice click the drop-down arrow and select Create Statement.

Note: there are three types of customer statements depending on your customer needs. For more details about, you can also check out this article: Create and view customer statements. 

Let me know if you have other questions or need further clarification with this. I'll be here to assist you anytime. Take care!