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Sound problems *should* be rare these days, and of the ones that still exist, they are likely related to suspend/resume. Those are driver issues which are largely out of your control, but see the documentation with the pm-utils package for details on handling those issues.

alsaconf used to be needed to set up sound cards in linux, but even that shouldn't be needed in recent linux distributions - everything should be handled automatically.
alsamixer can be used to change the volume.
alsactl store is used to save the volume settings.
alsactl restore is used to restore the volume settings. This is automatically run on boot, so you usually won't need to run this command.

There is one tip for the Sound Baster 5.1 cards: sometimes you want to MUTE digital out so you can hear on all the speakers; in alsamixer, you just press M on the Analog/Digital Output Jack item.

For change boot ordering for your sound cards just create /etc/modprobe.d/sound.conf and put these lines into it:

options snd-hda-intel index=0
options snd-usb-audio index=1

Replace 'snd-hda-intel' to your card module