Yes, use the Apple Software Restore app. I think you get it when you download Darwin. To clone a volume, you just have to drag the volume over the ASR icon, I think, and then you can choose the settings in the app.
In OS 9, I used ResEdit (file->get file info) to make all of the aliases (etc, usr....) immediately on the partition visible. From there it's just a matter of selecting all of those files and copying them to the new partition. (after you finish, you may want to make the files invisible again.