Lock the tracks that you don't want affected. Right-click at the left of the track and LOCK TRACK.
The dotted lines show up on overlays. If the overlay (higher track) image is smaller than the lower track you should see them both (picture-in-picture) and can position the overlay by dragging the overlay image. Or manipulate it with the handles in the preview screen. Mouse over the handles (dots/squares) - a pop up should appear to indicate what each does.

Of course. Save Project File AS routinely, giving it a unique # or name, so as not to overwrite prior saves. Using Save Project Files (no AS) will overwrite. Then you can restore a project to the state it was in when saved. Just double-click the VPJ file (which isn't playable).