I am working up a new 'sticky' to address this problem. What I have found so far is that CWM 6.0.1.x and TWRP 2.3.x.x are not compatable with the new Android 4.2.x version ROM's. They are fine with 4.1.x ROM's.
You must first flash CWM 6.0.2.x or TWRP 2.4.x.x to not end up with the nested /0/0/0 directories and duplicated files filling up your virtual sdcard when flashing an Android 4.2.x ROM.
And the file structure for your 'virtual' sdcard is actually in /data/media. The directories /sdcard and /storage/sdcard0 are just mirrored symlinks that do not contain duplicated data.
Now when you do flash an Android version 4.2.x ROM, your 'virtual' sdcard is moved from /data/media to /data/media/0. And that is the extent of what I know for sure so far. I assume that the symlinks become /sdcard/0 and /storage/sdcard0/0. I do not know if your backup of an Android 4.1.x ROM is still easily seen with even the proper recovery nor do I know if the original structure is restored if and when you restore said backup.
I am still trying to find out from others the things I don't know for sure because I still don't want to try out any of the newer rom's. Partially for this same reason as you, and partially because the only new feature I like is the 4.2 camera; I don't like the look of the 4.2 clock, nor am I attracted yet by the rest of the 4.2 features I've read about, even in a Sourcery ROM.