If you want to "uninstall" a container, so that its not longer part of the docker-compose.yml file, you have the possibility to use the menu.sh script, uncheck there the box of the container you don't want any longer. Afterwards you press Enter and a new docker-compose.yml should be generated.
However the generated file still has the old containers and settings in it. Going again into the build menu in the menu.sh script, the check boxes you unchecked before are then also active again.
Current workaround:
The only way to get a correctly generated docker-compose.yml is to navigate to the services folder in the IOTStack installation and delete the docker-compose.save.yml there. Afterwards you can run the menu.sh script again and check/activate all the boxes/needed containers again but let the not wanted containers unchecked.