I haven't started on my project yet, so I am glad to read some more information here.
@stormy: could you please add a bit of documentation and/or links to (english) documentation about how to put the bootloader on the atmel? Personally I haven't done this before; my Arduino's already had the right bootloader. I would like to know what the recommended uploader would be (maybe with a link or picture?) and what the recommended procedure would be to upload this.
Thanks for opening my eyes about this @magpern