Once your customer pays the invoice, you can now record their payment into your QBO. You can utilize this resource for the complete steps: Record invoice payments in QuickBooks Online.
You can always count on me whenever you need help with your invoices or QBO. I'll be more than happy to back you up anytime!
I understand the importance of having a late fees option in your settings. However, this feature is only currently available in the US QuickBooks version.
With this, I recommend using a third-party app to help you apply and calculate late fees for overdue invoices in your QuickBooks Online.