Where do you put your template override files? I am trying to get Drupal to recognize a template override that is a theme hook suggestion.
However, I don't know how to get Drupal 7 to recognize it.  

Specifically, Drupal commerce allows for the override of a customer order using the template file
commerce-order--commerce-order--customer.tpl.php

I don't know where to put this.  

I tried putting the file in my own theme directory, and clearing the cache. But it didn't recognize it.  Do I need to add something to the .info file of my theme?

I DID GET THIS TO WORK when I put the template in the main theme of the site, namely the omega_kickstart template directory. But this is not ideal for upgrading.

Finally, I tried making my theme a sub theme of omega_kickstart thinking it would override then, but that didn't work.
When creating new templates for your theme you need to name it to match your theme.

You'll want something like:

YOURTHEMENAME--commerce-order--customer.tpl.php