First of I am a total newbie with arduino and the "real" hardware programming. Did some BasicStamp tough and worked my way through some of the arduino tutorials. I have a STK500-Evaluation board lying around and was wondering if and how I would be able to use that to load the bootloader onto avr chips, I got an arduino board as well so boot-clone would probably work as well, I guess. Does anybody have a clue how the wiring on the STK500 will have to look and how to do the uploading? Thanks for any help.
It should be possible. There's a tutorial that explains how to configure the stk500 board, although you might need to some extra work to get the right command line (or check out the hardware/programmers.txt file in the Arduino distribution, you might be able to create an entry for the stk500).