So how do you add consoles? I have a Heavy Cruiser ship with 2 engineer 1 tactical and 1 science currently
You can buy them from a vendor or from the exchange. Obviously, Engineering consoles will only go in Engineering slots, so on and so forth.
Engineering Consoles are most geared around improving the performance of your ship; boosting power levels, raising resistances, increasing your hull repair, etc.
Science Consoles boost your Science stats so your Science abilities are more effective.
Tactical Consoles improve upon your weapons. You can get consoles that do +XX to an energy type (Phaser, Tetryon, etc), to a weapon type (beam/cannon/mine/torpedo), or to a projectile type (mine/torpedo).