The Arduino IDE (development environment) works really well but for some special occasions, it preferable and more enjoyable to rely on a good programmer to successfully transfer your code to the microchip. The Arduino Playground is explaining on this page a method for using the programmer directly with the IDE. You modify the preferences.txt file and all.
I prefer not having to edit the preferences.txt file so I don't have to quit/relaunch the application all the time. Here the method that I'm happily using (thanks a lot Massimo for showing it to me). It works magic for programming the Arduino Bluetooth. Uploading sketches over Bluetooth is not very reliable and so frustrating. With the programmer, it works 100% and it's fast.
I'm using the USBtinyISP AVR from AdaFruit. It works great and has direct support in AVRdude.
avrdude -c usbtiny -p m168 -e -U flash:w:/tmp/build#####/name_of_sketch.hex
— camille moussette 2008/08/23 12:10