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Buy nowWelcome back, @office-fireprote.
You are on the right track to receiving the payments and excluding the downloaded bank deposit to avoid duplicate transactions in QuickBooks. I'll share some information about attaching a single payment to multiple invoices.
QuickBooks Online (QBO) doesn't allow you to link a single payment to multiple invoices. You'll need to receive the payments on each invoice and make sure you select undeposited funds from the Deposit to drop-down. This way, you can deposit the payments in one transaction. Once done, you can now match the deposit to your bank feed transactions.
However, if the single payment is coming from your bank feeds, you can match it to multiple invoices by opening the bank feed transaction, then clicking Find match.
You may want to learn more about categorizing and matching transactions in QuickBooks. This article will guide you through the process: Categorize and match online bank transactions in QuickBooks Online.
Come to this post if you have other concerns or follow-up questions about this. I'll be around to provide further assistance.