I looked for it here on the boards but could not find an answer, so sorry if this ahs been covered before. Do you use the Crew rating only or can I use my Player Characters BS to fire the ship weapons, including but not limited to Torpedos.

Yes, player characters (aka "Explorers") can perform Shooting Actions, and they use their own Ballistic Skill.

Each player character can perform a single action during each turn of starship combat. As some of the actions available cannot be performed by NPC crews (this is covered in the expansion books i believe) it makes sense to let your crew cover mundane tasks such as manouvering the ship if no immediate stellar phenomena poses a threat and the players using their actions on things like focus augury, lock-on and shooting actions.