Invoices remain in an open state until the balance is cleared either by recording payments or applying open credit notes to the invoice balance. This Knowledge Article describes creating and managing payments (where a customer has actually paid you money). 

To record a payment against an invoice:

1. Navigate to your Order Management >> Sales Order. Select the Order you wish to edit. Click the Create button and select Payment from the drop-down.

Select the Invoice, Source of Payment and Date. You can also add a Reference, but that's optional. When you are done, click the Create Payment button.

Another method to create payments is to open an invoice and add payment like so: