Colour coding your section will add a stripe of colour on the separator page as well as in the index.
To add colour to a section, first you will need to select your desired section.
On the right-hand side of the screen, clicking "Properties Explorer" will display the properties of the selected section. Here you will find the colour settings.
With your new colours applied, this is what the Sections & Documents window will look like:
Once the bundle has been created, your index page will show the colours you have selected like so.
Each separator page will also show the selected colour.
These are the only places in your bundle the colour will be visible, it will not apply the colour to any of the individual documents in the bundle.