re: sounds, same as for map objects, you need to use a mod to get a general-purpose sound entity. check the entities under the "Sounds" section of Quoth:
http://tomeofpreach.wordpress.com/quoth/tutorial/
Another mod option if you want source code is Rubicon Rumble Pack, see the devkit in the first post:
http://www.celephais.net/board/view_thread.php?id=61077 , it has both ambient_general (sound entity) and misc_model (mdl decoration entity).
Most of the stock quake sounds are 8-bit, 11025Hz. Also most engines (including the originals) mix everything at 11025Hz. You can use CD-quality 16/44 for custom sounds and ask the player to launch the engine with "-sndspeed 44100", but note that most engines use a bad resampling algorithm so the stock sounds will sound bad in that case.
The last, annoying, bit is to make ambient sounds you have to add some unusual metadata in the WAV file to make it loop ingame. I can't find a tutorial off hand but try searching func for "loop wav" or something in google. Basically, you insert loop markers in an editor like CoolEdit or Goldwave, but it can be fiddly to get working.