I decided to encode my entire collection with FLAC. I'm ripping the CDs with EAC to wav, each folder is a different album.
Monkey's Audio Gui would be very useful, since it supports Subfolders, and I know it is possible to "hack" it so FLAC can be used as the external encoder, though it's not in the external encoder list.
I followed the intructions at the official FLAC webpage, but it opens a MS-DOS windows and nothing happens.
I probably made some mistakes, since i found the instructions a bit confusing:
I copied flac.exe and flac_mac.exe to the external folder, deleted \external\wavpack.exe and \external\wvunpack.exe, and then renamed flac_mac.exe to wavpack.exe and another copy of flac_mac.exe to wvunpack.exe
Then, via Monkey's Audio Gui, I've chosen to compress using wavpack, and a blank MS-DOS windows pops up.

What's wrong with this procedure? I don't want to use EAC to encode to FLAC on-the-fly.

Thanks in advance.

Dunno, works for me (WAV to FLAC v1.1.0 replacing WavPack like you did).

Did you check to make sure your binary will encode from the command line? I had one compiled version that didn't like my machine.

I was unable to configure it properly.
I ended up looking for another frontend for FLAC, and I found one which i believe is not listed neither in rarewares nor flac's official webpage.
It supports several compression levels, subfolders, cuesheets, tags, etc...
It can be found here.
Thanks for your suggestion anyway, Destroid.

Edit:
It is listed in FLAC's official webpage

I am sad. It seems like many times I can get processes working but others can not. Truth is I never tried encoding FLAC with MAC's frontend before and it worked flawlessly the first time

No offense, but if you quit trying on the first failure then I wonder what implications you are (unwittingly?) trying to make

I thought there were no alternatives with subfolders support but the Monkey's Audio Gui. While trying to hack it, I found a better frontend and logically (i guess) i used it. If i hadn't found it, i'd probably figure out how to hack that damn thing.
Anyway, that quitting subject is an off-topic discussion, as well as your ability to get processes working at first time.

Oh yeah? Well, you asked the question about "How to use FLAC" so be that way.

<immature ON> Nah, nah, I got it working and you didn't, ppbbtt! <immature OFF>