Are you talking about the router plate in your table? Yes it needs to be flush with the table top. The smaller insert plates that fit in the opening around the router bit need to be flush with the plate and the table too. There are corner brackets with set screws in the center and screw holes at each end that you can mount under the table across the corners of the router plate hole that the router plate sits in . You screw the ends of these to the underside of the table diagonally across the corners and then turn the set screws to raise the plate until it's level with the table top. A little blue Locktite on the threads will keep it in position, yet allow you to adjust it again, should you ever need to. Some tables have similar methods of leveling the plate while others have set screws in the plate corners that you turn down from above to lift the plate above the rabbet that the router plate sits in. Both ways work well.
Most of the insert plates seem to fit flush with the router plate well, and level with the table surface. Mine doesn't quite fit level, so I've added some blue masking tape to the underside of these to lift the inserts slightly to level them. It's Ideal to have the entire table, router plate, and the inserts all perfectly level with each other so your work doesn't catch an edge anywhere when you slide it across. Do what you need to get your table top, router plate and insert as level with each other as you can. Using your router table will be a nightmare if you don't.
Charley