Microcontroller firmware installation
RepRap has a Motherboard that is the overall controller of the machine. Each extruder has a subsidiary controller. The motherboard and extruder controllers have to be programmed. This page tells you how to do that.
Programming the Motherboard
The C++ program to be loaded into the Motherboard is in the directory mendel/firmware/FiveD_GCode/FiveD_GCode_Interpreter of the download.
In that directory there is a distribution configuration file called configuration.h.dist. Copy that file to a new file called configuration.h. The reason for this copying is that, when you download a new version of RepRap, you may not want to over-write your personal configuration file.
Run the Arduino Development Environment and load up the sketchbook mendel/firmware/FiveD_GCode/FiveD_GCode_Interpreter/FiveD_GCode_Interpreter.pde. Your new configuration.h file should appear as one of the tabs.
Click on that tab and read through the file. It is extensively commented and gives instructions on what to do to configure the firmware for your particular RepRap setup.
Plug the USB<->serial cable you made up on this page into the six-pin connector on the left edge of the Motherboard as shown. Make sure you get it the right way round. The RTS connection (which you should have coloured green) goes to the top end of the Motherboard connector labeled "GRN". The ground connection (coloured black) goes at the bottom, labeled "BLK".
Plug a USB cable into the USB-B socket, but don't connect the other end to your computer yet.
In the Arduino Development Environment select Tools->Board->Sanguino.
See also the Generation 3 Firmware page.