I felt the same way with multi-installs, however I gave it a go the other day and made it work.
If you don't want to use the mod enabler then don't. Just have one install called GW & one called NYGM in your programs folder(place shortcut for each on desktop). Then use the excellent MULTISH3 program to make certain that you save games don't get muddled up.
Multish3 found here
http://www.subsim.com/radioroom/showthread.php?t=98608
Note. Don't forget to rename your desktop shortcuts.(my mistake first time round)
Dan