Important note: in the tutorial I imply that the layers as shown in rep host are numbered the same as in the g-code. This is not actually the case. the gcode generally starts with layer 0 as the first layer, while rep host uses layer 1 as the first layer. Therefore if you want to switch colors on layer 5, search for layer 4, not layer 5. I have uploaded a fixed version of the document, but if you downloaded the first version please replace it with the updated version. Also, while Repetier host does allow you to visualize the paths, and select the end/beginning of the layer, I have found this does not always work well so this method should be more reliable as well as not depending on Repetier Host.
I was asked by a friend of mine how to do multi-color prints on her Solidoodle, so I decided to write up a step by step instruction for her. Figured I would share it with everyone.
Included the kitty simply because thingiverse needs a stl file, but it is a good first try.