Hmm, so I may need to modify lynxer, or find a new utility... But at least the AUDIO_IN line is free, as I don't expect to use EEPROM. Thanks!
lynxer is available for 1024, 2048 and 4096 bytes/block called lynxer, lyxner2 and lynxer4 (guess what the numbers mean). but yes if you want to use a different ROM layout you have to rewrite stuff.
the src for 1024 byte version is flying around on my harddisk, for 2048 or more you have to rewrite it. Ask when you need it.