If you are going to go with only 2x cannons then you want to use Dual Cannons not Heavies. This is due to global cooldown (1 second for all cannons) and self cooldown on Heavies (3 seconds for just that cannon).
I also recommend Photon torpedos because they have a higher dps just not as high burst.
The 3x Heavy Cannon setup is really amazing though. In PvE you will be amazed how fast you take down a huge warship with Rapid Fire alone. Sometimes my torps just don't hit.