Starting from WPS 6.1 you can create a Theme or Skin in separate .war file and install it on portal. You dont have to modify the wps.war any more. I followed the Infocenter Instructions for Creating a new theme and skin to create MyTheme.war and MySkin.war along with my own version of DeployTheme.xml that i can use to deploy both MyTheme.war and MySkin.war. Attaching those files below[>
First install MyTheme.war and MySkin.war as enterprise applications from the WAS Admin Console and then execute the DeployTheme.xml as xmlaccess script.