Dual Extruder Setup
The first thing you'll need to do to get dual extruders working is to edit the configuation.h file in Marlin to uncomment line 7 (approximately):
(Delete the first "//" to uncomment)
// #define RIGIDBOT_DUAL_EXTRUDER //Rigidbot Dual
(For info on editing & uploading firmware see "Getting Started/ Firmware" http://rigidtalk.com/wiki/index.php?title=Firmware)
Extra Trivia (not needed to get started): You can specify the X and Y offsets between nozzles in configuration.h (around line 357 & 358) but most people choose to do that in their slicer instead. Using the slicer settings has the advantage of being easier to adjust (no reflashing of firmware each time). Note that the slicer offsets don't override the firmware settings, but are added to them, so you'd normally want to use one or the other. It's possible, however, to put an initial value in firmware and then use the slicer settings for fine tuning. For example if firmware sets the X offset to 44mm, but it later appears the exact value should be 43.5mm, a slicer offset of -0.5 would correct it.
Open Repetier, select the Slicer tab, make sure Slic3r is selected in the slicer box, click Configure. After the Slic3r window opens (may take quite a few seconds) select the Printer Settings tab, General, and set Extruders to 2. You'll then have menu options for Extruder 1 and Extruder 2. Click Extruder 1 and set Extruder offset to 0 for both x and y. Then click Extruder 2 and set Extruder offset to x=44 and y=0 (assuming you have your extruders installed facing in opposite directions- if not just measure the x and y distances between your nozzles and use those numbers). After you do some test prints you can measure any mismatch between the printed stuff and adjust the offsets accordingly. Finally, select Print settings/Multiple Extruders and you'll see input boxes for choosing which extruder to use for Perimeters, infill and support. Note that the only valid numbers here are 1 and 2 (not 0 and 1; even though some versions of Slic3r will seem to accept a 0 it won't slice correctly) This part is just for using a different extruder for support material, so for two color prints using merged stls leave everything set to 1.
To merge multiple stls for two color prints, click File in Slic3r and select "Combine multi-material STL files". Select/open the files you want to use and then click cancel to exit the selection process. Filaments/temperatures are selected and slicing is done in the Slic3r Platter window, not in Repetier Host (click the "Export G-code" button to slice.) The resulting gcode can be loaded into Repetier for viewing and printing. See http://www.thingiverse.com/thing:124450/#instructions for additional instructions and a sample print.
Click on the Machine dropdown menu, select Machine settings. Set Extruder Count to 2 and click OK. The Machine Settings box inexplicably goes away and you'll need to pull it up again (Machine menu/Machine Settings)and now there will be input fields for Extruder 2 offsets in the lower left corner. The nominal values for Rigidbot are x=44 and y=0. If your subsequent prints display gaps or overlaps between the extruder outputs, adjust the offsets accordingly. To set temperature for the second extruder, look for "2nd nozzle temperature" under the "Basic" tab.