To mark the centerline, set a compass to span something more than half the width of the leg. Draw an arc from corner of the leg. The point where the arcs intersect will be on the centerline. With a centerline point on each end of the leg, place a scribe on the point, slide a straightedge up to touch the scribe. Do the same on the other end. When you have the straightedge positioned so that you can touch both points with the scribe, and in each case it is touching the straightedge - without moving the straightedge - scribe the line. Use scribes, rather than pencils or pens, because they make more precise marks.
The next day, cut it flush. Use a block plane to ensure it truly is flush. This will be the top of the bottom layer of the bench top, so gouges aren't a problem. (Wiping up glue with a damp cloth can lead to stains and finishes applying unevenly. That won't be a problem here, either.) But bulges and bumps are a problem - they will keep the two layers of the top from matching up evenly.