Just wanted to make a short info post about connecting AVR-STK500 and Atmel Studio 6 and especially the part where some processors are missing from the device list.
The thing is you need to add a couple of .xml files for the processors you'd like to program. The correct folder is located in YOUR_INSTALL_DRIVE\Program Files (x86)\Atmel\Atmel Studio 6.0\tools\STK500\xml. There you need to edit an xml with a text editor by changing the default name of the .xml to the pattern of the other xmls and edit the processor name inside. The rest should remain unchanged. Restart the Atmel Studio 6 and you should be good to go.
Example xml for ATmega328P (which is missing from the device list by the time of writing) is below.
<?xml version="1.0" encoding="UTF-8"?>
<avr-tools-part-file xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="../../schema/avr_tools_part_file.xsd">
<tool name="STK500" type="com.atmel.avrdbg.tool.stk500"/>