Invoice paid but quickbooks is still saying its overdue how do I mark them as paid

Nice to have you here, @simonhall-garden. Let’s go over your invoices and ensure you're able to mark them as paid.

I’d like to verify if the payment is linked to the invoice. If not, that’s probably the reason why it’s marked as overdue. Don’t worry, we can review them one by one.

Let's start by reviewing the applied payment to all of the invoices in QuickBooks Online (QBO). You’ll need to make sure that the invoice and the Receive Payment transaction are linked. Otherwise, you can delete it and transfer the payment to the appropriate one.

Here's how:

1. On the left pane, go to the Sales menu.
2. Select Invoices, and locate the invoice in question. 
3. Under Payment Status, click the 1 payment link and click on the Date hyperlink.
4. Choose the More tab and choose click Delete.
5. Select Yes to confirm.

After that, enter the payment again to the correct invoice. See this article for the detailed steps: Record an invoice payment.

On the other hand, we must associate the payment with an invoice if it is recorded as a bank deposit. By doing so, the transaction will be marked as paid. To learn how to do this, refer to this reference: Link a bank deposit to an invoice in QuickBooks Online.

You'll want to pull up the Invoices and Received Payments report to keep track of all your invoices and the payments that go with them. Simply go to the Reports menu, and then choose the said report from the Who owes you section.

I've got a link here that provides you with articles about managing customer payments: Manage payments.

Please come back and keep us posted on your progress in receiving the payments of your invoices. It's my priority to ensure your transactions are recorded accurately.