For Websphere community edition or Geronimo refer to the Guidelines in the OFBiz documentation : http://docs.ofbiz.org/x/Ah
Else to generate configuration files from the templates in a sub-directory of the templates directory just run something like (from the ofbiz.home directory):

java -jar ofbiz.jar setup test

All template files in the given sub-directory, in case "test", will be processed and put in a corresponding sub-directory of ${ofbiz.home}/setup.