Hi Barfuss,
You're asking a tough question!
Adding audio and video in HotPotatoes is not 100% the same as adding audio and video to Moodle or to Moodle through HotPot and through QuizPort, (as Deborah found recently) i.e. there are some differences that people need to be aware of. We all want to have THE one and only universal method but it's not happening yet.
So, the official tutorials (http://hotpot.uvic.ca/howto/audio.htm) tell you how to insert a flash player for the Web using their player, or another one. Players, however, don't differ much in that they should basically play the sound by using just the minimum necessary code. I have a small collection of players and the minimum code for each is downloadable (including the player).
Here we come to filters. If you want to include sound in Moodle, you can use the Moodle filters and the players that go with Moodle. Moodle uses filters to serve you the sound with a player. The code differs slightly in the URLs.
You can tell Moodle not to use filters and use the player you want and the one which you upload.
HotPot and QuizPort have 3 or 4 players available and you can use the square bracket notation (if you don't know or don't want to write the player embed code). Or you can tell HotPot and QuizPort to serve your hotpotatoes exercises with your player, in which case you also tell the Module (in the settings) NOT to use the HotPot filter; or you tell the Module to use the Moodle filter.
People who tried using javascript to dynamically display the player and the sound found that it's not working, for various reasons. So most of us now go the simple way: inserting an object with the minimal code for their players (without any filters) or the square bracket notatin method provided by HotPot and QuizPort (with the HotPot/QuizPort filters).
Hope this clears some of the confusion.
(I feel I should offer some examples, though.)
Cheers
Stan