Hi Rodrigo,
The 3D Shade Calculator that is part of SAM's Detailed Photovoltaic and PVWatts models calculates a set of time series beam irradiance shading factors based on your drawing of the active surface and nearby shading objects like trees and buildings. The active surface represents the photovoltaic array. When you close the shade calculator, it populates the time series beam shading loss table input in SAM with values representing the reduction is solar irradiance caused by shadows on the array.
The shade calculator does not read any inputs from SAM, so you have to be sure that the active surface you draw is consistent with the inputs on the System Design page. For the example you give, if the tilt angle on the System Design page is 23 degrees, then you should set the active surface Tilt property to 23. You should also make sure the active surface's Azimuth property matches the Azimuth value on the System Design page.
The GCR (ground coverage ratio) on the System Design page is a way to represent space between rows of modules in a rectangular array with more than one row of modules. It is used by SAM's self-shading model to calculate shading losses caused by one row of modules on a neighboring row. To model self-shading, you do not need to use the 3D shade calculator.
Best regards,
Paul.