I'm not sure how much you know about Source, so I'll start from scratch.
All data (materials, models, sound) is stored in GCFs, maintaining the same folder structure as a mod, you can think of it like an archive file. Everything is still held in folder like /materials /maps /sounds but it saves a lot of space. So for example when you download SourceForts, you don't download all the data that comes with HL2DM, just the additional custom content.
To get back to the point, if the sound you want to change are default Source engine sounds, you'll need to use
GCFScape to open the correct GCF file. And then export the sounds file you want, retaining the directory structure into:
SourceMods/sourceforts/sounds/
You can then edit these files normally. The custom sounds (mainly Khuskans voice) are all stored in
SourceMods/sourceforts/sounds/ctf