In order to encode an image sequence with audio you need to:
Create a folder including the files of the sequence (Jpeg, PNG or Targa)
Add the audio file (.wav) in the same folder
Audio files (.wav) that have been tested and successfully encode in a sequence are the following: 8bit/1ch 16bit/2-8ch 24bit/2-8ch 32bit/2-8ch
Start the Engine and ZooKeeper
Navigate to Media page
Open the settings and make sure that "Import Audio" is enabled
Hit the "Upload Files..." button (top right)
Navigate to the folder you just created and double-click on one of the image files
Select to import the sequence as a Video
Your sequence has now been imported as a video which includes the selected audio.
Now, in order for WatchFolder to "Read MediaMap Info From File Name" you just have to follow these instructions here without renaming the audio file.
Note: Make sure that the audio file is always of the same length or longer than the video. If the audio file is shorter than the video the remaining time will be filled with something that sounds like a glitch.