It depends on setting of isolation mode for registry keys and directories:
Full
Modification to virtual elements fo to the sandbox
System elements cannot be read or modified
New elements will be created in the sandbox
Merged
Modification to virtual elements fo to the sandbox
Modification to system elements fo to the system
New elements will be created in the system
WriteCopy
Modification to virtual elements fo to the sandbox
Modification to system elements fo to the sandbox
New elements will be created in the sandobox
:-)