Configuration
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e16menuedit2 autodetects your currently active E16 session and 
uses the environment variable $ECONFDIR to read from your E16
config directory. If you use E16.7.x or earlier this variable isn't
set and e16menuedit2 read your config from ~/.enlightenment. In E16.8
and later $ECONFDIR is set to ~/.e16.

You could also edit your config files from another E16 version if you
redefine $ECONFDIR:

ECONFDIR="/home/user/.e16" e16menuedit2

If you've some old menu directories in your E16 config directory 
you could use -m parameter (see: e16menuedit2 --help) to force
the new menu structure.