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How do I mark invoices as paid without it making the bank balance and QB balance not match?

I marked the invoices as paid and then deposited the money but I split the check between two accounts. I called QB she told me to delete the deposit in my check register and now it shows the invoices as not paid. I called back and they said to add it back but it doubles my account balance in QB. How do I mark these invoices as paid without it being marked as a deposit into my account in QB? Please HELP