Hi Rajat,
Have you activate "Payment Reference"field in GL Group field status variant to Optional?
After that, you can create one new layout or change existing layout which add "Payment reference" field.
Go to tcode O7Z4S, create new layout by copying from existing one
Then, click on Insert after... button, add Payment reference field, then Save it.
Go to tcode F-04, choose line layout you created, you will see Payment reference in here
If you still cannot do it, please let me know.
Regards,
Julie