ScreenAware looks at the focused (active) Window unless that active window is very small (e.g. a confirmation popup) in which case it would also consider another window which occupies >80% of the total screen.
In a dual-monitor-setup with e.g. spreadsheet maximized in one screen and browser in the other, ScreenAware would always consider the focused (active) window.
That said, if a project relation for a window can not determined, such time may if it is "wedged" in between recognized time slices, be attributed to that project as well.
So in the above spreadsheet/browser example: if the spreadsheet can be related to project A and for the browser URL no relation can be found, switching focus from time to time would lead to both window activities being related to project A. If you would stay solely in the browser for longer than a few minutes, that time would show up as "No project" though.