I am also an ecommerce seller. I am writing this as per my understanding.
The ecommerce seller should declare his sales in GSTR1, whether it is B2B or B2C. Further Govt also wanted us to bifurcate the sales through e-commerce operator (E) and also other than e-commerce (OE) separately. For the sales through e-Commerce Operator, we have to declare the GSTIN of the operator. Now, the E Commerce Operator like Amazon, Flipkart etc are bound to declare your transaction through them to the department. Later the GSTN would match your records and Amazon / FK records to tally the same. So both seller and Operator need to declare the sales to GSTN.
However, due to technical issues in the portal, the above separation has been put on hold till notified by Govt. Till such time, we have to club both ECom and OE Sales under OE Sales. The source of this info is from the Webinar Recording from GSTN in Youtube. This issue is shown around 24th minute. https://www.youtube.com/watch?v=8hOyBLvIE-I.