Depends on where the scratches are in the refinishing process, under the stain (you don't see them until stain is applied or in the finish coats. Fixing a coat of finish, varnish or other clear coat, is fairly easy; sand with 220 or finer grit to remove the scratches, do not sand through the finish, and apply 1 or more new coats of finish. If the scratches are in the wood, visible only when stain is applied, then the stain and scratches must be sanded off, basically starting over with new clean wood.
I used Howards Restore a Finish and it did not completely cover the scratches. I just used a cloth. I didn't try the steel wool with the Howards Restore a Finish. Would the steel wool work better. I ordered some wood elixir to try and cover the scratches.
You can add more coats of Howards or do some light sanding with fine sandpaper or steel wool then add another coat. Watco is another product that might work better for you, has a little more pigment when compared to Howards Restore-a-Finish.