Hi,
we are using the onDemand Version of Jira, but we have also tested the dowload version. We have seen some differences between the both Versions, the interfaces are quite different and you find some option and configurations on different menus. The most how to's and white papers are for the download version, so that we don't find some options like they are shown in the whitepaper.
Maybe you can help us and tell us something about the differences.