How do I manually mark an invoice as paid? My invoices are showing as overdose but customers have paid them.

Good to see you here, userkylie1.

You can create a Receive payment to manually mark the invoice as paid.

Here's how:

1. Go to + New > Receive payment.
2. Select the customer's name from the Customer drop-down list.
3. Set the Payment date, Payment method, and Deposit to (You can use the Undeposited Funds account to deposit the money later on).
4. Under the Outstanding Transactions, put a check mark on the invoice you want to pay.
5. Click Save and close.

Please see this sample screenshot for a visual reference:

For more details, you can read this article: Record invoice payments in QuickBooks Online.

If you receive bank deposits from your customer, check out this link on how to record the payment: How to link a deposit to an invoice

I'll be right here if you have any follow-up questions about recording the payment or other concerns with your QuickBooks Online account, Have a great day!