Navigator Basics...
Project Map = all the windows that ArchiCAD generates itself...
Each Story
Each Elevation
Each Section
etc.

View Map = Project Window + Attributes
Layer Combination
Scale
Pen Set
etc.

When you click on items in the Project Map, nothing but the window you are looking at changes. So if you are looking at your SITE Plan (for example) and you choose your ROOF story from the project map, you will move to that story, but still have Site Plan layers showing.

If you create VIEWS (in the view map) for SITE PLAN and ROOF PLAN, clicking these will reset all the attributes such that you are looking at the correct window, layers, pens, scale etc.

Views are REQUIRED to place drawings onto Layouts. So when you get to the Layouting portion of the Navigator and call up a sheet, you can only place VIEWS onto it. Even if you drag something from the Project Map, it will create a view (and place it at the bottom of your view map) before placing it on the layout (sheet).

So.... EVERYTHING should make it into your VIEW MAP. You will have to create all your views by setting up your Window, scale, layers, etc and right click inside the VIEW MAP. You have an option then of SAVE CURRENT VIEW which you can NAME and ORGANIZE the way you like. For example, you can keep all Plans together in a folder and all elevations in a separate folder.

There is SO much more to the navigator, but this should get you started.