This product is far too complex to attempt to learn without study and/or training. The User Guide (the 4,000 plus page one) has a thorough explanation of the Project Navigator, and Paul Aubin's Mastering ACA 2010 (945 pages) contains a great overview of PN. Not enough has changed since 2010 to make this book, or its last successor, obsolete.
The Project Navigator is ACA's file management system, a kind of "smart" Windows Explorer. When you start a new Project by copying an existing one, it unfortunately does not include the drawings in the copied project. Unless the Commercial template project is close to what you actually need, I would suggest starting a new project from scratch. Even if it is, I would still minimally go through the process on a small project first to get a better understanding of how and what you control.
The Project Navigator palette contains 4 tabs: Project, Constructs, Views and Sheets. Your drawings are all contained in the Constructs, Views and Sheets, and the Project tab is your manager, and where you define your levels (one of the first things you will want to do). If your drawing contains 3 floors, you will have a minimum of one construct drawing for each floor, and your roof drawing also will be a separate construct. In the Levels section of the Project Navigator, you enter the floor elevation and the floor-to -floor height of each level in your project. You do not do any dimensioning or documentation or printing in your Construct drawings, and you do not do any "modeling" in Views or Sheets. You say that you can't create second floor plans without first creating spaces. What you need to do is first make sure that you have set up a level for your second floor, create a new construct drawing and assign it to the second floor level, draw your interior walls, doors, etc. At that point, you can create spaces based on your drawn geometry. In the Properties palette, you have an option to specify 2D, extrusions or freeform for each space.
In the View tab, you create View drawings that contain xrefs of one or more Construct drawings. For example, if you want to see an exterior composite of your entire building, you create a View drawing that contains all the constructs you want to see. When you create a new View drawing, you specify which drawings to include. You can also detach drawings you don't need afterwards, as well as just drag and drop construct drawings into your view drawing. You also create View drawings for documentation and dimensioning. The Sheets tab is for printing. You drag and drop (xref) Construct drawings into View drawings, and View drawings into Sheet drawings.
Everything you see and everything you print in this product is based on seemingly infinite settings, so if you don't learn it in some sort of organized method, you are going to continue to be very frustrated.
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