You need to have the model designed so the text or logo (or whatever you want a different color) has a flat surface that can be oriented parallel to the build tray, either as a positive or negative image. The final color needs to be at least 2 layers of model material thick to prevent the base color from peeking through. When you are satisfied with the design export your .stl file for processing. This example will use Catalyst for the Dimension line, but the process is similar using Insight for the Fortus line.
As usual, you will open the .stl file, set your build properties and orient the model. Depending on the object being made you will have the test/logo as wither a top or bottom surface. In this case I chose to orient the CAPINC logo as the top surface.
The pause will be at the start of the selected layer, so you need to choose the first layer of the part you want in a different color rather than the last layer of the base color (reverse this if building the model upside down).
If you have different colors that you want to use, you simply need to have each color end on a different layer (at least 2 layers apart) and insert a pause for each new color. This model shows that technique.