Hello Aparna,
if you use S32DS 1.2, you should be able to compile and download the program correctly.
Unfortunately, Processor Expert (PE) is not available for this project, because PE is available for SDK base projects only. But there is no SDK available for any MPC56xx microcontroller.
When you look into the reference manual, in chapter 3, there is pin description, which tells you, what is the functionality for
each pin (https://www.nxp.com/docs/en/reference-manual/MPC560XPRM.pdf ).

When you combine this with the figure you shared, you can see, how is every pin configured.

For example PHASEA0 is A[0] Port pin, so you can check, what is the PCR0 configuration.
Description of the PCR register can be found in chapter 11 SIUL.


Regards,
Martin