Allocating 1 payment to main account and sub account invoice?

Thanks for coming to the Community for help, @Rafiq11.

I appreciate you providing detailed information about your concern. There are two possible reasons why the error message shows up:

• The second invoice is for a sub-customer of a different parent customer. 
• The Bill with parent isn't selected on the sub-customer’s profile.

Let’s verify the setting by going to the Customer Information window of the sub-customer.  Here’s how:

1. From the Sales menu and select Customers.
2. Look for the parent customer and make sure the sub-customer is under it. If not, select the supposed to be the sub-customer name to make the necessary changes.
3. Click the Edit button next to New transaction.
4. On the Customer Information window, make sure to place a checkmark in the box next to Is sub-customer.
5. Select the parent customer on the drop-down box and choose Bill with parent.
6. Hit Save to record the changes.

See the article What does the bill with parent feature let you do on invoices? for more information.

Now let’s go back and perform the steps to apply the card payment. Choose the parent customer on the drop-down for both main and second invoice to appear on your end. Mark the box next to them and save the transaction.

Check out this article for the detailed steps: Record a customer payment.

Reach out to me if you have any additional concerns. I'm always here to help. Have a good one!

Hi Rafiq

Just to confirm from the last comment you posted have you then been able to receive the payment and match it in the banking section now?If you are in the sub customer receiving the payment and it is billed with parent then it should also impact the customer parent balance.