There's actually like 4 different layers to Linux Audio these days on Debian based systems.
You've got Alsa, Pulseaudio, Jack, and currently they're running something called Phonon.
They're all quite hackable and can be beaten into shape with sufficient googling and command line editing, but they can be stubborn at times, requiring multiple reboots to get the changes to stick sometimes.
Congratulations young man. You're learning the joys of Linux Administration on the job
Like I said, installing all the KXstudio packages with a meta install and then running KXStudio Welcome from the System Menu will take care of most of the configuration for you.
After that you can tweak as you like.
One of my favorite things about Linux is that no matter how much you abuse it you can pretty much always recover the system even when you f*** things up real bad
I've been running Linux only systems since 1998 so I've learned a trick or two
Gary