Starting from Atmel Studio 6.0 beta, You can see whether the Atmel USB installation failed / succeeded, status of it. Though the device manager to an extent tells you about the status of the device i.e working/ not working, you can inspect some logs to understand the reason for failure (or) send it back to an support engineer for debugging the failure.
1. Go to the installation path of Jungo USB driver. typically it would be Program Files\Atmel\Atmel USB\usb32 for a 32-bit operating system and Program Files (x86)\Atmel\ Atmel USB\usb64. or the one you would have manually configured, and find a log file by name atmelusb.log, that shows the status of the Jungo USB installation that ran while installing Atmel Studio.
2. The DIFx framework in windows generate a separate log file that specifically will have the technical reason for a failure. This log file will be available in \windows\inf\setupapi.dev.log
Hope this helps