The problem is that most banks provide downloaded invoices/reports in formats that only work with Quicken. What you should do is purchase an Excel Add-In that will allow you to convert the downloaded data into Quickbooks format.

Here is a great company that provides such Add-ins:

http://www.bigredconsulting.com/

I contracted them to enhance their Excel Add-in further that dynamically adds in the appropriate columns in the Excel spreadsheet and saves it into a QuickBooks INF file. Nice little app that has saved the accountant of one of the companies I am contracting with in terms of massaging the downloaded bank file.
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Buh Bye!

Cheers,
Me