Ok guys,
Here we go;
I installed the game on my D:\ partition and so is there GWX of course;
D:\Silent Hunter\game files + GWX. (JSGME already activated mods).
Computer restart.
Then I created the D:\Commander folder and installed the SH3 Cmdr.
On top of everything and yet before I configured the programme, I copied SH3 cmdr files into it.
Again restart.
Finally I chose my Cmdr preferred settings and only to find out that there is no go.
Commander shows the correct "D:\Silent Hunter\" folder in SH3 path.
That's all I know.