If you don't have a sound pack yet, then your sounds folder should be empty. HT changed the sound file system a while ago, so that all default sounds are one file.
If you want to install a sound pack, just download one, unzip it, and put the files into your sounds folder. They will override the default sounds. With sound packs, you should have the 'multiple folders and wavs floating around' that you described.
EDIT: Also, none of the sound packs have been updated for the new planes yet. So, if you want custom sounds for, say, the Spit16, then you have to copy one of the other Spit folders (I don't know which is closest to the 16, so I just used the 9) and rename it to "Spit16". The same applies for any other planes that don't have custom sounds, like the new Corsair (in fact, I think that's the only other one besides the spit16).