Sounds like you do not understand the difference between Views and Viewpoints, as far as layer combos not changing when you switch between elevation and plan...
And creating separate anno layers per story sounds like you came to ArchiCAD from a 2D CAD background? Stories segregate information already, so there is no reason for per-story anno layers.
These are very basic issues that should be understood before beginning one's first 'real' project... have you had any hands-on training in ArchiCAD?
Karl
AC 28 USA and earlier • macOS Sequoia 15.3, MacBook Pro M2 Max 12CPU/30GPU cores, 32GB
One of the forum moderators