To Compile modify the MAKEFILE:
change this to your arduino bin folder
ARDBIN = E:\arduino-1.0.1\hardware\tools\avr\bin
change this to match your com port
ARDCOM = COM5
When done compiling you should see a AtomCNC.hex file.
To Upload simply run UPLOAD.bat.
CHANGES:
7/23/12 : New Setting to lock/unlock motor.