I think the best approach would be to model the LDR sensors in Simulink as well. I believe you are using Simscape Multibody (from your previous questions) so you can place a "light source" approximating the sun and use the Transform Sensor to meaure angle and distance from this light source and then model their voltage behaviour. You can even move the light source using something akin the Point On Curve Constraint to mimick the day passing.
Then I would feed directly the the voltage difference of the sensors to the PID block. In the end the PID act on the DC motor and continue to act until the input to the PID block is 0. So I would simply use the voltage difference, but in order to model and tune it in Simulink with this approach you do need a model for the LDR sensors and the sun position.
Just my 2 cents, good luck.