When you pay an invoice, or apply a credit against an invoice, they become allocated. If you're unsure which transactions are allocated to each other you can check the Payments and Allocations. 

Review the allocation of payments, receipts, and credit notes to invoices.

1. Click Sales or Purchases.
2. Locate the invoice to check allocations for.
3. Click the invoice or credit note to open it. 
4. Select the payment link under the Amount Paid value. This opens the Payments and Allocations option.
5. Here you can view all payment links related to the invoice or credit note.
6. Select the link in the Amount column for more details.