Stage Manager seems like it is intended for use when you don't have any virtual desktops set up, you just use one. As you can then manage your windows into small groups akin to virtual desktops. Combining the two, though, was odd. I tried it for all of Ventura's life cycle and never really got used to it. Most of the time the window I would want was never on screen. I'd merge it into the current group, but then that largely defeated the point. So for Sonoma, I've turned it off. I might re-examine it in the future if it gets some improvements.