If you've still got the sander on site, go ahead & stain anywhere to pic a color, then run the sander back over the stained area with whatever final grit you sanded. If you don't still have the sander, you can use a belt sander with the same final grit paper. Don't sand smoother than the rest of the floor or it could potentially not stain the same as the rest. The stain is not going to go very deep at all.
One other thing, be sure to sand past & feather your sanding out so as not to create a noticable dip.
One other thing, be sure to sand past & feather your sanding out so as not to create a noticable dip.