You'll have to edit a SoundPak.py file manually; they are located in your BC directory, in scripts/Custom/Autoload. When you open the file you'll see something that looks like this (note that this is an example. As I don't have the mod that you're describing I don't have the exact sound pack you need to modify):
#######################################################################################
# Custom Weapon Sound Plugin #
# Created by BC - Mod Packager #
# Date: 4/10/2002 #
#######################################################################################
# #
import Foundation
import App
# #
#######################################################################################
# #
Foundation.SoundDef("sfx/Weapons/mvam_photons.wav", "PromPhotonTorpedo", 1.0)
Foundation.SoundDef("sfx/Weapons/mvam_quantum.wav", "PromQuantumTorpedo", 1.0)
Foundation.SoundDef("sfx/Weapons/mvamprom_phaser_a.wav", "MvamPrometheus Phaser Start", 1)
Foundation.SoundDef("sfx/Weapons/mvamprom_phaser_b.wav", "MvamPrometheus Phaser Loop", 1)
As you can see, you've got, after the standard "Foundation.SoundDef", "(sfx/Weapons/'name of file', 'sound name'). So you'll need to locate which sound files are for the ships you need, and ensure that they're properly setup in the sound pack. After that, you'll go into the hardpoint (for the phasers) and make sure they're named properly on each individual beam weapon. Using this MVAM Prometheus sound pack as an example, you see how at the end it says "MVAM Prometheus Phaser Start/Loop", in the hardpoint for the MVAM Prometheus, you'll see each beam array has a line for the sound effect ("MvamPrometheus Phaser").
For any torpedo weapons, you'll ensure the sound corresponds to what's in the sound pack in the torpedo script, so in this example, if you open up the "DurPromPhotonTorpedo.py" file, you'll see in there for the sound it is listed as "PromPhotonTorpedo".
Hope this helps. Feel free to let us know if you need any more guidance.