Wow thanks for all of the quick replies!
I am pretty sure I have not flashed the bootloader to the atmel chip yet. When you guys refer to boot loader do you mean the Marlin or Sprinter code? or are you refering to something else all together. Hopefully I am not too lost at this point and in my case a bootloader that I can use could be this Marlin code.
This is what I have attempted to do so far, I am going to try and keep this simple:
1. I downloaded and installed arduino 1.0.1 on my WIN 7 machine. When I connected the Arduino via USB, WIN7 said the Arduino did not install properly. I went into the Windows device manager and manually pointed to a set of Arduino drivers and everything said it loaded sucessful. I am a bit doubtful at this point but there are no more errors in the device manager.
2. I have extracted the marlin code to a folder on my desktop.
3. I launch Arduino on my Windows machine and select FILE OPEN 'MARLIN.PDE'
4. Do I need to select my board type? ??? MEGA 2560?
5. If I try to compile it I get an error compiling. c:/users/mbailey/desktop/arduino-1.0.1-windows/arduino-1.0.1/hardware/tools/avr/bin/../lib/gcc/avr/4.3.2/../../../../avr/lib/avr6/crtm2560.o: In function `__vector_default':
(.vectors+0xb0): relocation truncated to fit: R_AVR_13_PCREL against symbol `__vector_44' defined in .text section in c:/users/mbailey/desktop/arduino-1.0.1-windows/arduino-1.0.1/hardware/tools/avr/bin/../lib/gcc/avr/4.3.2/../../../../avr/lib/avr6/crtm2560.o
I am really just floundering around at the moment...sorry guys if I seem like an idiot!