I need to convert a huge colllection of FLAC files to MP3 and would like to do the best quality Batch Conversion possible with as few headaches as possible.

So far I am looking at Foobar, dbpoweramp and VUPlayer

I've started testing dbpoweramp but it seems that I have to go into each folder and select the files.

Is there a way that I can just point a program to the master folder and have it convert all of the files in all of the subfolders?

Yes there is. Foobar2000 at http://www.foobar2000.org
I downloaded the "Special" installer, as opposed to the Normal and Lite installers. It has the most stuff bundled.

Now load up foobar & go:
Playlist > Add directory.

This will add all your songs, despite any being in subdirectories of that folder.
Press Ctrl+A to select them all.

Now, right-click and go:
Convert > Settings (to configure your encoder settings for the first time)
Under "Output file name formatting" I have changed to the following (but your tastes/ preferences might be different). This is just my preferred directory structure:
It will output nice & neatly that way based on your already-tagged FLACs.

Under:
"Output Presets"
you would choose:
Commandline Encoder: LAME --alt -preset standard
(or whatever your encoding preference is here)

You have to make sure your LAME.exe (or whatever mp3 encoder you choose) is in foobar's program directory, or tell it where it is with the EDIT button there.
Don't have LAME? Get LAME 3.96.1 here:
http://www.rarewares.org/mp3.html
...then extract it to C:\Program Files\foobar2000 (or wherever you have foobar installed).

Another useful thing to change - while ur there in Preferences in foobar - is to go to the left hand side window and click on "standard inputs" and under "mp3 tag writing" choose ID3v2, because it's not selected by default.

Now press Save All. Close.
You have configured your mp3 encoder and you'll never have to worry about it again. Now just:

*Ctrl+A to select all files again. This time just go:
*Right-click
*Convert > Run Conversion
*Your encoder settings can be changed there if you like. Otherwise, press OK.
*Now select your output directory and bob's your uncle.

Mass conversion of FLAC to mp3 (!), without having to manually go into each directory (& all outputted neatly in the directory structure you choose).

Have fun.

Thanks so much CB!

What if it doesn't give you the option to edit when choosing your decoder?