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Thanks for reaching out to the Community,usertom.
Based on the scenario, let’s manually pay the invoices and deposit the payments. On the Bank Deposit page, we’ll have to enter the fees to net off the amount. I can help show you the process.
To record the payment:
To deposit:
If you’re unable to create the fee item, follow the recommended steps in this article: Add service fees manually to invoices.
Once done, you can match the downloaded bank transactions to the deposit. I've included an article to help you in the future. It outlines the complete steps on how to combine transactions in QuickBooks with a bank deposit, input a partial payment for an invoice, etc: Record and make bank deposits
Feel free to post a comment below if you have additional questions. I’ll get back to answer them for you. Enjoy the rest of the day.
Thanks so much, I’ll try and give it a go and come back to you
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