Yup, i got to work with it while playing silent hunter 3. You have to put the files you need to overwrite to "mod" the game in a special folder UNDER the game's folder. For example, if your path is c:\games\IL2 then you should have a folder with a path of c:\games\IL2\mods. Under that one, you then need to make an additional folder called c:\games\IL2\mods\409beta
Inside that one you'll place the files changed by the patch. Take care to use the EXACT folder structure though. If you need to replace a file in your missions folder for example (i think you don't, i'm just using it as an example), the correct folder structure would be a copy of the game's default one: c:\games\IL2\mods\409beta\mission\filename.mis for example
After that, you can run JSGME (as the tool is called) and you'd see two columns. One is listing the available mods on the left, the one on the right lists the activated mods. From then on it's simply a matter of selecting a mod and enabling it by moving it to the right hand side column.
Here's a link to the subsim forums showing a screenshot of the interface:
http://www.subsim.com/radioroom/showthread.php?t=105421
Here's another link with instructions on how to make it work with SH3.
http://forums.ubi.com/eve/forums/a/t...2/m/3461029123
Since you know how to do it manually i doubt you'll have any trouble substituting the correct folders to make it work with IL2. Cheers