There are two ways to access the Firmware Upgrade dialog. To access it manually you can select Tools→ AVR Tools Firmware Upgrade from the Atmel Studio menu. When you open the Programming dialog, the Firmware Upgrade dialog will appear automaticly if there is a firmware upgrade available for any connected tools.

Firmware upgrade can also be achieved using the command line utility: avrfwupgrade. For details on how to upgrade tools firmware using this technique, execute avrfwupgrade -h