As per the Provision of Section 39(10) of the CGST Act 2017, "A registered person shall not be allowed to furnish a return for a tax period if the return for any of the previous tax periods has not been furnished by him."
Hence you cannot proceed to file your FORM GSTR-3B for the month of October 2020 without filing GSTR-3B for the September month. It is not allowed under the GST Law.
Yes Sir that can be done but an alert message will be coming to your registered mobile number and email address that you have filed GSTR-1 for a particular tax period ( say Sep'20 ) but your GSTR-3B is pending...