Once you have built your jtag ice you will need to program it with the bootloader. You then uses AVR studio to upload the latest firmware into your ice. I have attached the files you need - This will work with a Kanda200 style programmer - it is one of the easiest to build!
Ok, so I'm trying to get the Evertool-Light thing to work. After making the PCB, I guess I have to download evertool.hex into the ATmega16 connected in it and I'm good to go right?