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If you search in the XML Publihser Administrator responsibility for the Templates the are getting displayed already (Sales Order RTF, Sales Agreement RTF, ....etc)
you can able to find out the Template Data Source which is of .XSD extension . So if you create a new Template and Assign this .XSD based Data Definition to your Template then automatically your Custom Tempalte will come in the Layout list of transaction Type Setup Screen.
Check this and let me know if you have any complexities in finding these.