A few comments, Tricia.
First, it's important to note that SuperDuper! is a "one-way" copy program -- it doesn't sync. So, if you make a change to the PowerBook and then copy from the Mac mini to it, you'll lose that change. (That might be obvious, but it's important.)
If you want to keep the two machines in "sync", you probably only want to do that in specific folders -- Documents, say, and your Desktop. To achieve that goal, you might want to use a program like FolderShare, which is free, and works quite well -- see
http://www.foldershare.com.
As far as SD! is concerned, you haven't done any thing wrong. It just sounds like the old "memorized" drives are different than they used to be, so SD! can't automatically restore them. Just click "cancel" to the prompt, and re-select the new drives, and things should be fine.
Does that help?