When we receive a payment this is allocated against the main account. Balance is updated but the payment does not show on the sub-customer - Why?

Hello there, lconlon.

On the sub-customer's profile, let's make sure to select the Bill with parent option. That way, the payments will reflect both on the parent and sub-customer. 

1. Go to Sales tab and select Customers. 
2. Click on the sub-customer's name. Select Edit button.
3. Under Is sub-customer, select Bill with parent.
4. Select Save.

Also, let's make sure to select the sub-customer under Customer drop-down when creating the invoice. It won't reflect on the sub-customer if we've selected the incorrect customer.

Once done, let's delete and recreate the payment you've processed. This is to ensure that the Bill with parent option will take effect.

You can read this article as your guide: What does the bill with parent feature let you do on invoices?.

Keep your posts coming if you need more help.