You want to open the Marlin_RAMPS_EPCOS_i38.ino file in the Arduino IDE. That is the best way to edit and then upload Marlin.
Starting at line 378 of pins.h, you should have changed this:
Code:
#define TEMP_0_PIN 13 // ANALOG NUMBERING
#define TEMP_1_PIN 15 // ANALOG NUMBERING
#define TEMP_2_PIN -1 // ANALOG NUMBERING
#define HEATER_BED_PIN 8 // BED
#define TEMP_BED_PIN 14 // ANALOG NUMBERING
to this:
Code:
#define TEMP_0_PIN 15 // ANALOG NUMBERING
#define TEMP_1_PIN -1 // ANALOG NUMBERING
#define TEMP_2_PIN -1 // ANALOG NUMBERING
#define HEATER_BED_PIN 8 // BED
#define TEMP_BED_PIN 14 // ANALOG NUMBERING
And then move the Hot End thermistor connection to the last thermistor connector.
One thing I noticed is that the source they provided doesn't include some of the libraries often required to compile Marlin. The U8glib library being one of them. Your LCD controller won't work without it.
I have Arduino IDE version 1.0.5-r2 installed and the firmware compiles just fine. You can download it here:
https://www.arduino.cc/en/Main/OldSoftwareReleases#1.0.x
After it is installed, you will need to have the U8glib library installed so you can use the LCD. See this page:
http://reprap.org/wiki/RepRapDiscount_Full_Graphic_Smart_Controller
and this page:
https://code.google.com/p/u8glib/wiki/u8glib
Installing the library is simple. Just put the folder in your "Libraries" folder or import it using the Arduino IDE. Restart the Arduino IDE and you should be good to go.
I hope this helps. You really want to have this installed and be somewhat comfortable with editing the Configuration.h file. You can make some good changes to the firmware which you won't see in the changes allowed by the Repetier Host software.