There is a folder in every mod and version of Sins called Sound. The files there are in OGG format but (I think) MP3s will work too? (anyone?).
All you need to do is swap your files for the ones there using the names of the ones you replace.
If you create differently titled sounds or add additional ones you will have to update the totals in the SoundMusic.sounddata file in the GameInfo folder in the Sins directory on your PC.
I believe you'll need to convert them from BIN format (encoded) to TXT. The SoaSE Weebly can give you a step-by-step oin that and harpo has a tool kit to do conversions with some instructions as well.
There is also a SoundEffects.sounddata and a SoundDialogue.sounddata file in the GameInfo folder for other sorts of sound (dialogue and effects).
Audacity can convert and edit all your sounds in all the formats you'll need and it's free. Notepad++ will help you editing the text data files and it's free too.