When you say you have programmed the PID controller, using MATLAB, what exactly do you mean? Are you still using the Mindstorms environment to program the EV3, or are you using a MATLAB/Simulink Support Package? Also, how are you developing your PID loop?
Lastly, have you seen this example already?
Not exactly what you are trying to do, but fairly similar in terms of setup.
Lastly, scaling the PID probably is not the best thing to do. You would want to re-tune it with different levels of aggressiveness and confirm that the motor effort does not exceed 100 (in this case). Just directly scaling the output allows the poles of the closed-loop system to become unstable, even if the original PID controller was stable.