The QuickBooks 2006+ Instructions state that you should save these files in the Payer's Directory.  To find out where the data is in the 1099-Etc program, you can go to the Main Menu, select Help>About 1099-Etc.  To the left of the screen, the working directory will be listed, where all of the payer folders should be.  If you did not save the files as instructed you will need to recreate then and save them to the correct directory.