Let's say you have a compiled hex file you want to upload to your microcontroller via Little-Wire. To do so, first you have to download WinAVR package for Windows. For linux, you can type sudo apt-get install avrdude . After you set up your environment, you can use the command below at your terminal:
avrdude -c usbtiny -p m8 -U flash:w:main.hex
At this command, we assumed that name of the compiled hex file is "main.hex" and we are using Atmega8 as target microcontroller. To fix this command for your target microcontroller, you have to know what is the part number of your device. You can find that list at here.
For linux, in order to use Little Wire as a programmer, call avrdude with root privileges. For example:
sudo avrdude -c usbtiny -p m8 -U flash:w:main.hex
You can also look to the detailed tutorials written by Ladyada:
http://www.ladyada.net/make/usbtinyisp/avrdude.html
http://www.ladyada.net/learn/avr/avrdude.html