Hi again @Canberk,
To use the MCSPTE1AK144 with encoder you must follow the Getting Started with the S32K144 BLDC/PMSM Development Kit.
In the Plug It In section, place DEVKIT-MOTORGD jumpers J9, J10, J11 to position 1-2 for PMSM application (Because only for PMSM application is the encoder function available, in this case MCSPTE1AK144_PMSM_FOC_2Sh).
In my case I left J8 open to establish a 5V voltage level for the encoder.
Connect the encoder to JP1 as shown in the following figure:

In the Build section, before clean, build, debug and load, change the ENCODER macro to 1 in the main source code.

Then in FreeMASTER, set the resolution of your encoder in the Sensors tab.
Finally, Start application and Set speed in the App Control tab, then in the Project Tree/Encoder Sensor/Speed you will be able to visualize the Speed Encoder in the dynamic graph.
Regarding the MOTOR_PP_GAIN and MOTOR_PP_SHIFT macros, you don't need to change them, since these are motor parameters, not encoder parameters.
Hope it helps you!
Have a nice day!