<p>Where can I find a good Rails newbie-friendly reference about generating rails models with foreign key relationships?  </p>

<p>I've found some pages indicating that you should add <code>has_many</code> and <code>belongs_to</code> to the relevant models to specify these relationships, but haven't seen any instructions for getting the scaffolds to generate the correct controller and view code that would reflect these relationships.</p>

There are a bunch of StackOverflow questions asking for newbie reference materials. I recommend that you start with the two Peepcode screencasts:
Rails From Scratch Part I
Rails From Scratch Part II
They do a great job of visually introducing you to Rails 2 development. Then, I'd recommend you pick up the Rails 2.1 PDF by Ryan Daigle, to get the hang of the 2.1 features not covered in the screencasts.
I'm not sure what you're driving at with your question. What are you expecting the scaffolding to do? Create multi-object relationship links automatically? That's something you have to start layering in yourself....and as you do so, the scaffolding starts to be replaced with a real application. The scaffolding is just a starting point: it's not meant to guess what your inter-object relationships are going to look like in the application.