Am I on the right track?

I am new to Unity3D having used XNA Game Studio and Torque previously. I am used to an different structure or a game loop and find Unity a little overwhelming at first in its architecture. But what I seem to understand is that it all revolves around scenes. Scenes are the driving force. So I might have a scene called TitleAndCredits that displays the appropriate info, one called MainMenu, one called OutsideMansion, one called Inside MansionFirstFloor etc. All my game objects will be attached to the scenes with scripts attached to the game objects and scripts attached to the scenes. What I am having trouble figuring out is how the main scene is determined. for example in the 3rd person shooter and bootcamp, what is the first scene displayed and how do you tell that. Am I correct that Unity is scene driven?

Are there any good tutorials that cover game architecture and how to structure the files etc?

The first scene displayed is the one on top of your ‘build stack’ (build settings). As for the hierarchy, you were close, though scenes can not contain scripts (or any other component). A basic hierarchy tree would be this:

                                           Components such as scripts:
Project > scene1 > prefab1 > gameObject1 > Mesh Renderer
                                         > Mesh Collider
                                         > Rigidbody
                                         > MyScript
etc..

Hope this helped! =)

-Patrick