Hi,
i think you should clone JA Raite template into 3 templates, ex JA Raite Green, JA Raite Yellow. (After cloning, you need to goto cloned folder, open templateDetails.xml file and change name params
[<name>JA_Raite_Green</name>].
And then, you can open clone template in backend, set Default Style to color you wish and assign menu items for that template.
With this way, One menu item will have colored style.
Other way, you dont need clone template, for each menu items, you have to switch it to External Link, and append params ja_color=COLOR NAME to menu Link.
Hope that helps