You can use your colors to brand your app in several different places.
First, via your home screen. This will allow you to change the color of the 'tap here to check in' display:
Next, via 'Buttons' on the left, you can select the color of each button you create. Start by clicking 'Visitor Buttons' and click 'edit' next to the button you want to change:
Now you can select a variety of customizations for each button, including color!