Ben, A Simulscan programmers guide has also been added to Launchpad and can be found here. At the bottom of the guide is a note about the programmatically copying the default templates. Your app would need to get an instance of the SimulscanManager (which sets up some permissions), then use standard java file API's to copy the templates where you want them.

Hi Ben,
Default templates can be copied from the device itself, you can find them here: /enterprise/device/settings/datawedge/templates

In the next version of EMDK there will be an API that allows a calling application to copy the latest default templates to an application specified directory, this should make access to these templates much more convenient.

Unfortunately you will not be able to modify the default templates using template builder, these templates were custom made outside of template builder to cater towards specific use cases.
Dave