Hello Andrew,
At this point, PCB and Schematic Export work on a single-supply design. When you construct your power supply tree in power architect, you can currently export the individual designs, not the whole project. Your suggestion is very good and we have noted it. While I cannot promise this feature, but we will surely take a very serious look at this request.
I sincerely thank you for using the WEBENCH tools and I loved getting this suggestion. Users like yourself make our work worthwhile.
Regards