The STK500 does not have a USB connection, and cannot be automatically detected by Atmel Studio. So it must be added to the list of available tools before it can be used by the Device Programming window.
To add an STK500, right click inside the Available Tools view, select Add target…, and select the STK500 as the tool and the COM port your STK500 will be connected to.
Press the Apply button and the STK500 will be displayed in the list of available tools.
Note: An STK500 that has been
added will be visible in the Available Tools view event even if no STK500 is connected
to the specified COM port.
If you want to remove STK500 from the list, you can right click on it and select Remove from the context menu.