Ok, so I've created separate emulator.cfg for each version of CSBwin I'm using and that works fine.
But now I have troubles with Der Clou again. After a reboot I can't start it from ES anymore, I get:
Executing: /opt/retropie/ports/theclue/theclue
ERROR: Module Dsk: Open :./pictures/bubble.fnt
And it seems to be a path issues, because I get the same error when I try to run the binary from the menu in Raspbian.
I can run it when I go to the directory manually at the command promt. So my guess is that the script not goes into the directory and thats why it can't find the datafiles anymore. Weird thing is, that I can run it from ES after I started it once from the command promt.
Also i just noticed that I can't save because of restrictions. D: