When you get paid for the invoice you will need to reconcile the invoice against the transaction for it to show as paid. Please follow the steps below on how to do this.
First, find the unreviewed transaction in the Transactions tab 'To review' section.
Next, click on the transaction to open the categorisation panel.
Finally, select the outstanding invoice to allocate the transaction to the invoice.
Once you do this, you can then mark the transaction as reviewed to reconcile.
After this, the invoice with show in the Invoices tab as paid with the transaction linked.