The simplest way to start a new site is to import an existing one, delete the parts you don't want, and create any new bits that you do. At the most extreme this would be a case of deleting everything below "Alfresco Quick Start/Quick Start Editorial/root/" apart from "collections" and "index.html" and then building up your own section structure. For documentation about how to develop a WQS-based webapp, the WQS Developer Guide should help. If it doesn't then please come back to me, and let me know what you feel is missing so I can address it.
I agree that the "create from scratch" option should be slicker - perhaps we should simply ship an empty example along with the finance and government ones.