You don't actually load a Makefile onto an Arduino. The Makefile is used to build the part that does go onto the Arduino: the 'firmware image' or 'hexfile'.
The easiest way to handle it all is to use the Arduino Development Environment, which you can get here: http://arduino.cc/en/Main/Software
When you void a product warranty, you give up your right to sue the manufacturer if something goes wrong and accept full responsibility for whatever happens next. And then you truly own the product.