Would like to add google custom search to site, using this methodology:

http://digwp.com/2010/10/google-cust...o+WordPress%29

If I wanted to replace the default search and put Google CSE in the same location, where do I add search box code:
searchform.php
-or-
header.php
-or-
/functions/bfa_header_config.php

I always avoid modifying theme files. I would put the code in a widget and position with CSS.

be great if Atahualpa followed this paradigm:

http://codex.wordpress.org/Child_Themes

you can create a child theme with atahualpa

So if I copy Atahualpa and rename directory to act as a child and then in child theme's style.css do I merely add:

Template: Atahualpa

and then i can modify the files in the child theme?

You copy the style.css and change the title to something like

Theme Name: Ata 377 child

and you need the index.php . after that you can do what you want.

How does child now about parent without reference to template:

"Template: Atahualpa "

With your suggestion mean, when Atahualpa updates occur I will not need to modify bring theme updates into child?

You leave in the template name so your style.css will will start with

/*
Theme Name: Ata 377 child
Theme URI: http://wordpress.bytesforall.com/
Description: Configure your custom theme: Fixed or flexible width layout, with min/max width, 0 - 4 sidebars, very browser safe (incl. IE6), create custom widget areas, import/export styles (several styles included), color pickers, over 200 options. 
Author: BytesForAll
Author URI: http://forum.bytesforall.com/
Template: Atahualpa377
Version: 0.1.0
*/

Notice the 'Theme Name' line at the beginning and the 'Template' line towards the end.
You might want to read up on creating a child theme at wordpress.org

So when Atahyalpa 3.7.8 comes out change:

Template: Atahualpa377

to:

Template: Atahualpa378

In my child theme's styles.css?

That's the idea

Is it not possible to create a child theme that need not be modified everytime the latest ATA version comes out?

the child theme ties to the parent theme based on the 'Template: xxxxxxx' line and the xxxxxxx is teh name of the FOLDER in the themes folder. If you use the Wordpress automatic install and updating, the theme folder is Atahualpa so you would use 'Template: Atahualpa'. If you are doing manual installs and have multiple installs so your folder was Atahualpa378, then you would use 'Template: Atahualpa378' inorder for it to apply to that release (this means changing it each time you install a new release)

It is not so easy. How do you think the wordpress on my website's blog /www.homedecornest.com/blog .I don't know how to add the google custom search to my website too.

homedecornest: this forum is for users of the Atahualpa and Montezuma themes. If you want to ask questions, you need to use one of these themes.