I am using Windows 8 64 bit. I am trying to convert a bunch of .flac files into .wav and .mp3 files. Originally I would go through each folder import the .flac files into Audacity and then export them into another folder. This is taking forever because of the amount of .flac files I have and I am hoping for an easier way. What the folder consists of is one main folder, the artists folders, the album folders, and then the .flac files. I am wondering is there a way to use chains to load in the main folder and have all the files converted with the sub folders and the new formats in their proper folders? Please tell me there is my hand it hurts from the clicking!!! 
Sadly not. Chains are currently limited to processing files from one folder only.
If you know anything about writing BAT files you could probably adapt the script that I posted here (for processing files recursively through sub-folders using SoX)
I am not familiar with it is it difficult to comprehend? I am gonna check out your link because this is killing me. It will take me weeks to do it all the way I am now. Thank you for helping me.