Sonic boom physics are subtle and counter-intuitive. High level, you: (1) keep the airplane as small and light as possible (reduces total shock energy) (2) carefully shape the fuselage and wings, so the shocks don't combine as strongly

NASA and Boeing have a design that has the engines on the upper part of the wings saying it reflects most of the boom upward. (see ninth paragraph) https://www.nasa.gov/aero/centers_tackle_sonic_boom.html