In many cases windows are the same type throughout the home, although for some homes it is necessary to create a 2nd window systems. Many times this just depends on how detailed you are getting for calculating things like solar gain, air sealing, etc. In a hot climate it would help calculate the cooling load. In a cold climate with metal frame single pane windows, it would help calculate the heating load.

If some of the windows have a different type and/or different frame, you can separate those windows by creating a 2nd window system.

The example below is for a home where the basement windows need to be upgraded (system 1). Also notice that the basement level windows have no overhang, which in itself could be a reason to create separate window systems.

On the refine screen under Window System 1, you will choose Yes for the "Windows Improved?" question and you will edit the improved U Value & SHGC to match the new windows you installed.

For Window System 2, you will choose "No Improvement", so that those windows will be excluded from any improvements in the modeling.