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Child themes modifications

I am very confused about editing my style.css file.

Allan Cole says in his website “Why ditch Thematic? Using child themes allows you develop/customize themes really quickly however, the child theme structure created an extra dependency that caused lots of compatibility issues with the theme, Thematic and WordPress itself”.

Wordpress says: child themes are recommended way of making modifications to a theme because it does not affect the parent file of the theme, which I kind of like this better... but, I am still very confused... Any recommendations?
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  • I am using Autofocus (NOTE: this is his theme update that does Not use Thematic) and got a plug-in called: Child Theme
    It will show up in your Admin menu and creates a simple new theme then you can edit it's new stylesheet without modifiying the original Autofocus style.css.

    However, I am new at this, I have found some code I wish to change apparently cannot be changed on the style sheet, but rather, in the other files (php). I have not figured out how to modify the other php files while keeping the original Autofocus theme I duplicate the original php files onto my computer as backup before making any changes to the php files.....
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