With a simple feature you can set some automated action to be executed each time a site is created for a given template, and other options too.
This is done by creating a site definition.
Check out, download and install theme stapler (and theme changer if you don't already have a theme activating feature).
Actions can then be customized in file:
C:\Program Files\Common Files\Microsoft Shared\Web Server Extensions\12\TEMPLATE\FEATURES\ThemeChangerStaple\Elements.xml
Theme Changer Feature (separate download) (Recommended default)
now broken link