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Once you've made a setup.iss, you SHOULD be able to put a folder called 'Devices' in the same folder as your setup.exe. Put all your individual handheld devices in that folder, as their base executables, and your setup should install them all as it runs.
Found a good article from BlackBerry regarding re-packaging their software. Search for Repackaging the BlackBerry Desktop Software Installer in the Technical Knowledge Center.
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