Ecommerce Accounting

You can pass one single entry (State wise) daily for all B2C Supply with total amount and for B2B invoices you have to pass seprate entry (i.e invoice wise entry)

In GSTR 3B you have to report total Net sale after sales return (i.e net figure).
In GSTR 1 You are required to report B2C sale total figure net of sale return state wise..and for B2B invoices, reporting is invoice wise..
All this reported along with your other sale (not through e-commerce sale, both or same).