Bill in GST

yes you can maintain

In the same manner which you are showing now

u have to show both 's series invoices in gstr 1 

and in documents issued

u have to show both invoice series

YES YOU CAN MAINTAIN 2 SERIES OF INVOICE

AT THE TIME OF FILING GSTR-1 ENTER NO. OF DOCUMENT ISSUED FOR BOTH SERIES IN COLUMN 13

Yes, You can maintain serial number as your convenance (No restrection from department). 

If you may change the format by providing a written intimating the GST department officer along with reasons for the same.