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sorry, i did not get it . what do you mean by "read the barcode scanner "?
A barcode scanner is only something which is installed between your keyboard and workstation. That way it doesn't matter if you enter the code by hand or using the scanner: you click in the field which needs the code to be entered to get the focus on it, next you scan your code. The only problem might be that after scan there's no automatic submit, so you need to click a button then.
Did you try windows mobile device center or Microsoft ActiveSync?