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We can only split a downloaded transaction into multiple categories in QuickBooks Online. You can use the Receive payment feature to pay your invoice. Ensure that the account to use is Undeposited Funds.
Once done, use make deposits when you get back from the bank. Put a checkmark on the payments, select the bank account you deposited to, and ensure the amount in QB matches the actual deposit.
You can use these articles for additional reference on how to handle customer payments:
If you need any additional assistance with customer payments, I'll be here to help.