To add colouring, go to ‘Visual Effects’ tab, select colormap (by pushing Change button near ‘User Colormap File’) - you can find a lot of colormap files in PDF3DReportGen\samples\colormaps, on the same tab there is ‘Color And Elevation Binding’ group of controls where you have to turn OFF Automatic Attribute Channel check-box.
After this step, you can try to produce 3D PDF. It will use scalar values from first attribute (‘Color Array Index’ is set to 0). If you would like some other, you can define them by using ‘Color Array Index’ or ‘Color Array Name’ controls. You can find all available array names in Conversion Progress dialog after some conversion inside of lines:
Found New Attribute Array: >***<
Now, if you want to use one of these scalars, just enter one of these strings to ‘Color Array Name’ or its zero based index in ‘Color Array Index’ and push Convert.