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When you set up the sub-customer profile, you will have two options; Bill with parent or Bill this customer.
If you select Bill with parent, this means that the balances and the transactions of the sub-customer will be added to the parent customer profile. You can also use this link for reference: What does the bill with parent feature let you do on invoices?
Meanwhile, the transactions and the balances will not affect the parent customer profile if you select Bill this customer.
If you need additional help with setting up the profiles, please let us know. We'll be right here to further assist you.