The Prusa i3 offers the functionality to use different colors/materials for different layers. This feature is called Color Print. The Prusa website has a special page where you can upload you gcode file and specify the layer heights where the filament change has to occur. This may not work correctly in some cases, e.g. when there are multiple objects on the build plate and thus several places in the gcode file where the same height is mentioned.
I find it much easier and reliable to manually enter the filament changes. Identify the layer height in Slic3r (something that you would have to do for the website as well), then open the gcode file in a text editor and look for Z command. Simply step through the matches until you find the first Z command of the layer height that you want in the new color, and insert M600 before it (e.g. at Z1.250 below).
G1 X130.849 Y127.792 E-0.76000 G1 E-0.04000 F2100.00000 M600 G1 Z1.250 F6000.000 G1 Z1.750 F6000.000