You can not replace it as the default shell in window. If you did that all your desktop icons will go away, and some of the feature in Multi Commander depends on Windows Explorer.
It might be possible top tweak Windows Explorer so that when clicking on my computer or folder. Mulit Commander would open.
But I don't know exactly how to do this. It has something to do with changing HKEY_CLASSES_ROOT\Folder in the registry.
You can try google for that, But I do not recommend messing around in the registry like that, unless you really know what you doing. If you do decided to change things there. Make a backup first.