Hi Hari,
You are unable to change the primary object may be because its Case type is Automatic.
Their are following Case type:-
a) Automatically: for this clarification case is created automatically when EMMA transaction founds msg defined in the case cat in the application log.
b) Manually: for this we have to generate the case with help of BAPI by manually coding it.
If you still want to add your custom object you can add it as additional object by using same BAPI_EMMA_CASE_CHANGE and passing the object in "OBJECTS_ADD" table parameter which will show your object in same place where primary object is shown.
Or if possible you can change the Case type from Automatic to Manual but then you may need to write a code for creating BPEM case as it will stop creating BPEM case by reading application log.
Regards,
Rohan