How do you tell if a wire is "too long" or "too short"?
I vaguely recall someone having problems with 60 cm wires. Until you have something working, try to keep the wires 10 cm or less.
The auto reset seems like a likely culprit, how do I disable it?
For the Duemilanove, an approximately 120 ohm resistor from 5V to RESET seems to work well.
The Duemilanove contains a trace that can be cut to disable the auto-reset. The pads on either side of the trace can be soldered together to re-enable it. It's labeled "RESET-EN".
That would be a semi-permanent method and, as far as I know, has never been required.
You may also be able to disable the auto-reset by connecting a 110 ohm resistor from 5V to the reset line; see this forum thread for details. Is that it?
Go with that option. There are more details here...
And what commands, and where would I look to find them?
First, make certain you can run AVRDUDE from the command-line. In my case, I have to do this...
Or, if you prefer a great deal of typing, you can use a full paths...
C:\Arduino\arduino-0022\hardware/tools/avr/bin/avrdude -CC:\Arduino\arduino-0022\hardware/tools/avr/etc/avrdude.conf -v -v -v -v -patmega328p -carduino -P\.\COM14 -b115200 -D -Uflash:w:C:\Users\USER~1.001\AppData\Local\Temp\build4128319007689436592.tmp\sketch_aug23a.cpp.hex:i
A command like this should do nothing more than check the fuse settings (nothing is written)...
avrdude -v -v -v -v -patmega328p -cSTK500 -P\\.\COM14 -b19200