I prefer one Torp Fore and One Torp Aft. In PvE, I guess it doesn't really matter but in PvP, if you can't bring their shields down, torpedoes are useless.
Hmm I put RCS(turn rate improvement) on my Sovereign and in PvP just shoot with your broadside(4 beam arrays) and when the shield is gone turn a bit with either ur aft or fore torpedoes and fire away....
Heck I even put a single dual heavy cannon on my dreadnought just for the fun(and PvP with it and the cloak console, I know nuts but I'm enjoying it).
For STF I have chosen, like many others, a setup with two forward and one rear torp. This setup leaves space for five beams which is still nicely manageable. More importantly it doens't leave the ship threatened or underpowered against more maneuverable or multiple ships. Combined with Star Cruiser and a tanky mentality, you can blast large targets with all your weapons (except the rear torp ofc) while standing still, do a good job there and still be able to take on two or three Spheres on your own, dance a bit with them and kick their asses.
Ultimately, like also stated previously by others too, it's a learning curve that needs to be experienced by trying out different setups. It's not up to the gear how well someone manages, it's the style how he/she plays and how well his/her setup comforts that style. I doomed Dual Beam Banks not worthy of STF, but I am often seeing setups with multiple DBBs and they seem to be doing just fine. I didn't like long reloads of Tricobalts - still not uncommon sight. At this point I'm just replying for the joy of writing, sorry if it annoys someone.