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I accepted both (i) the payment debit from the linked Chase checking account, which was paired with the primary Chase credit card (Card A) sub-account and (ii) the payment credit to the Card A sub-account.
I then created two transfers of the allocable portions of the resulting Card A overpayment to the sub-accounts for Card B and Card C. All three cards now show the correct QB balances.
So it appears that when I pay the total credit card balance each month I'll need to manually transfer any resulting overpayment of the primary card to the other sub-accounts. It would seem that Chase and/or QBO could make this a bit easier. (For example, QBO could allow you to readily split a credit card payment amount sub-accounts when you accept the transaction.). But until then, this seems to be a work-around.