Hi @Aravind_Togaralli,
1. NXP always recommends using the latest SW release available. Right now, the latest release for S32K3 include:
S32DS 3.6.10 includes PEmicro interface debugging support version 6.2.1.
2. When importing an example, or creating a new S32DS application project, the respective debug configuration is generated. You can refer to the examples for the recommended settings, however, most important ones are 'C/C++ Application' path, device & port selected, and GDB Client executable path:


3. Yes, if you wish to debug the FRDM-A-S32K344 with an external debugger, you must use the J9 20-pin Cortex Debug + ETM header.
4. As detailed inside the FRDM-A-S32K344 development board user manual (UM12406), to enable this interface, jumper JP11 (OpenSDA voltage) must be removed.
5. You can refer to HOWTO Build a Project and Setup Debugging with GDB PEMicro Debugging Interface. Or you can refer directly to PEmicro: PEmicro NXP_Automotive S32K3xx Device Support.
For any specific function/configuration, you can try contacting PEmicro instead.
Best regards,
Julián