Link_tool = 0;
L(1) = RevoluteMDH('alpha', 0, 'a', 0, 'offset', 0, 'd', 0.0892);
L(2) = RevoluteMDH('alpha', pi/2, 'a', 0, 'offset', pi/2, 'd', 0);
L(3) = RevoluteMDH('alpha', 0, 'a', 0.425, 'offset', 0, 'd', 0);
L(4) = RevoluteMDH('alpha', 0, 'a', 0.392, 'offset', -pi/2, 'd', 0.1093);
L(5) = RevoluteMDH('alpha', -pi/2, 'a', 0, 'offset', 0, 'd', 0.09475);
L(6) = RevoluteMDH('alpha', pi/2, 'a', 0, 'offset', 0, 'd', 0.0825 + Link_tool);

I don't know if it is changed in last releases, but usually you define a SerialLink instance in you matlab workspace where the Simulink block is referring to. You ca do that in a regular script or in on of the callback functions of the Simulink file.
Erik