What worked for me was to ONLY override the nav-buttons within a view (even just the nav buttons on one side - left or right), like this:
<ion-view view-title="Main">
<ion-nav-buttons side="right">
<button class="button button-icon button-clear ion-ios-gear-outline" ng-click="changeSettings()">
</button>
</ion-nav-buttons>
<ion-content>
...
</ion-nav-view>
This worked perfectly, however it stops working when you try to put it in an ng-include or in a directive. So, I end up copying/pasting the piece of code to 3 different templates (because I have a screen with 3 tabs and I want to have these nav buttons regardless which tab I click). Yes that's ugly but it works.
When I tried the "ion-header-bar", it did NOT work for me, for my "tabbed" page (ion-tabs). What happened was it was then putting the header bar UNDER the tabs.
Probably I'm doing something wrong but i didn't bother exploring further, I sticked with copy-and-paste, ugky but the quickest solution.