El, you may already be familiar with these links (to help understand the CM software). I too had issues with it for some time and continued to use the in-game control assignments...until a squaddie walked me through setting up an easy map for IL2. Once I went through it, tweaking it and setting/reassigning controls was easy. I'd be glad to do the same for you if you would like.
Here's the first:
http://home.att.net/~stickworks/contents.htm
and of course the
Control Manager For Dummies (Remember to right click, save as 8mb):
http://www.ch-hangar.com/531_ghost/Dummies_Guide.pdf