You don't - you have to configure it all by hand.
What you want to do is change the default (global) settings. The specifics depend upon the actual application itself. However, there is always a configuration file someplace and a master set of stuff... so, like there is a user configurable icons set in ~/.icons , there are also /usr/share/icons and /usr/share/pixmaps which contain more globally available stuff. (eg, I can change the global firefox icon by changing /usr/share/pixmaps/firefox.png)
However, it will take some hunting around for everything you want to do.
1. you alter the applications global configuration file.
2. you change the default theme
Back to "automate" ... once you have the configuration you want, it can be moved to other machines easily enough.