I want to customize the Joomla 2.5 Atomic template as per design. But, as I learned that the customizations will be lost once I update Joomla. I don't want that to happen because I will be doing a lot of customizations and redoing that won't be a good idea after each updation.
I want my customized template to be intact even after Joomla updation.

So, can any one throw some light on how to achieve it?