We do also see the Enterprise do the same thing in "For The World is Hollow..." and the dialogue is more explicit:
KIRK: Prepare phaser banks one and two, Mister Sulu.
SULU: Aye, sir.
KIRK: Mister Chekov, get a fix on the missile's point of origin.
CHEKOV: Aye, Captain.
SULU: Phasers one and two locked in and ready.
KIRK: Fire phasers.
And both phaser banks
fired through the two forward ventral emitters. It would appear that two emitters can channel or fire energy from multiple banks simultaneously.