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:
nxf86756_0-1671672332885.png
In the Build section, before clean, build, debug and load, change the ENCODER macro to 1 in the main source code.
nxf86756_1-1671672350159.png
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!