Simply put, those messages are the generator telling you what it found...
The app/controllers folder already exists. The app/helpers folder already exists. The app/views/site folder did not exist, and was created
Your controller is the glue between the model and the views for that model...
Start a new rails project, and
ruby script/generate scaffold song artist:string duration:integer genre:string
and see what gets created (all sorts of wonderful things). Peruse the folder hierarchy and see what the parts are, and where they get created - songs controller, song model, song views, it's all there, albeit in a very basic format.
Many folks disparage using scaffold, but it's a great learning tool for seeing a fully build out example.