>We are exporting from a program that will ship the order, bill the customer, and collect payment. So I guess we will need to send and invoice transaction and a payment transaction.
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>What I am most concerned about is that if I export an invoice transaction into QuickBooks it can be edited and changed within Quickbooks!

Access to QuickBooks files can be controlled in two ways. A company's QB file can be protected by a password which must be supplied to open the file. In addition to that, different users can be set up and each can be assigned different permission levels. I know this feature is in QuickBooks 99, but I can't say about earlier versions. Look under "passwords" and "permissions" in the help file for your specific version.