Sorry for the lengthy post
You can't apply shellac over urethane, it will peel. You would have to strip off all the urethane first. As for the sanding of the surface it depends on the size of the spot, from the sounds of it you really should sand down the whole surface, then re-stain and apply your top finish of choice. If you try to patch it you will always see the spot. There are a number of techniques we use to hide small blemishes that need to be touched up on the surface but, this applies only to blemishes that as a rule of thumb are no more then the size of a small knot in the wood. First projects are always the worst, you are excited to do it and impatient to finish it, which is what gets us into trouble. The clear finish on the project takes more time then most think depending on what you are trying to achieve. I just completed a new Cherry desk for my computer the varnishing alone has over 60 hours of labor in it to achieve the result I wanted. As for the comment about Oak being a hard wood so the stain should not penetrate it to deeply while accurate to Oak being a hard wood, it is a very open grain wood so the stain does penetrate very deeply into it, it is this penetration of the grain that gives you the dark details of the wood grain even after sanding. My advice would be to take a deep breath relax sand done the surface evenly, then apply your stain to even it out and re finish with your choice of clear coat top finish. but take your time and don't be in a rush to complete it, we always seem to have time to do things over but never enough to do it right the first time. Finally the scratches you have are the result of the first sanding you did being having a to aggressive grit, the sanding marks run very deep into the veneer and trying to remove them you run the risk of sanding through the veneer. you are best to get it down as smooth as possible the suggestion of steaming it may help you will have to try it to see. If you have the opportunity go to a store called Lee Valley great store for wood working, and they are also on-line at leevalley.com you can find everything you need for your wook working and lots of great books on finishes and techniques.
Good luck
