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BigTex
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I bought and used an APP called Transaction Pro, installed the program/app and in the Target in program properties I typed "C:\Program Files (x86)\Transaction Pro\Transaction Pro.exe" /RECPAY3.

When I setup the excel worksheet, I when I applied a check payment from the customers for instance and I used the same check number but added ".001" to the check. For Example if check # 1108 paid four invoices from  four different customers I would show on the  Excel Worksheet Ck # 1108.001 on the first Line (row), Ck # 1108.002, on the second row, etc. I then imported the Excel worksheet (csv) into Quick Books. For example the columns looked like this: 

DateTypeCheck NumberApply to Invoice     Amount     Deposit To      Discount Amount      Discount AcctMemoAR ACCT

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