The concept that Ionic is running on is from my understanding single page page application. Where there the skeleton of the page(application) is created in the index.html from there you take out and replace the content with different views to navigate between different views.
if you need more in debt information check out this link
http://en.wikipedia.org/wiki/Single-page_application
Solving your problem of having different color for each view header look at the link below.