Hi Asu
For June you will have to create challan under category "Any other payment" for the month of June.
Alternatively if you have made monthly payments of April and May by selecting "monthly payments for quarterly returns", just fill up GSTR-3B and then after saving proceed to payment there you select create challan. A challan will automatically created for remainder tax amount.
You can use both methods. Both are valid.
Hope this helps.
Regards
Altamush