This is the problem with GST portal. They are not allowing to edit once clicked on submit. The only thing we can do is make payment and file return.
I do not understand logic behind this.
Government should have scrapped the idea of GSTR-3B and should have gone with normal returns.
They should have come with advance tax concept like income tax for first 2 months. Just pay liability and file normal returns in extended period.
Sorry to say but now you cannot do anything. If you do not pay tax and file your return, then penalty of 100 Rs. daily will become applicable to you.
It is better to pay and file return. Take input credit in normal returns and revise return if allowed later.