I started learning Ruby on Rails a few weeks ago, and I've found it a lot easier to get the hang of things and learn my way around by not using scaffolding, and generating the various parts from the command line (or macros in an IDE).
However, from what I can tell, when you use scaffolding to generate things, you think of it as generating a "resource", so you're only going to create one resource at a time, then add in the relationships by hand later.
However, the generate model command can create these relationships for you. Lets say you used scaffolding to create a Scale resource.
You could then do
ruby script/generate model GuitarString name:string scale:references
The scale:references will create a belongs_to :scale on your GuitarString model, but you'll need to add has_many :guitarstrings to your scale model.
The generate model command also creates a migration script for you and other files needed (fixtures), similar to scaffolding, but doesn't autocreate views or controllers or anything.
EDIT:
This is generally how you are going to want to do things - use the generate/model or generate/view or generate/controller or generate/migration. Most Rails developers don't use scaffolding, since its "one size fits all" rarely fits things perfectly. However, most rails developers do use the generate commands I mentioned - it saves time with creating helpers and fixtures by hand, and it gives each file it generates a basic template you can add to.
Several Ruby IDE's like JetBrain's RubyMine have macros that essentially perform these commands. In RubyMine you can do ctrl+alt+g, then enter another key corresponding to what you want to generate.
The belongs_to relationship can be generated by using the "references" word, as I mentioned. Others you will add in by hand.