[Taera]

If you use tactical combat, when you fire weapons you can deselect some of the weapons to fire them on other targets. you wont be able to do so unless you have multiplex, and even then the number of targets is limited.

For strategical combat, there is the damage percent. If the enemy is dead and there are still other weapons over the "percent" the ship will fire on other targets given it has multiplex.
Also ships can use their PDC as a weapon(meaning wont fire automaticaly but aimed) after firing on ships with the use of multiplex.

Hope that helps.