Question

Should e-commerce domestic companies register in every state? If yes, then what are procedure for registration in each state? And how can we file its GST Return?

Answer

It is clarified vide FAQ issued by CBEC reproduced below:

Question 7: Whether e-Commerce operator is required to obtain registration in every State/UT in which suppliers listed on their e-commerce platform are located to undertake the necessary compliance as mandated under the law'
Answer: As per the extant law, registration for TCS would be required in each State / UT as the obligation for collecting TCS would be there for every intra-State or inter-State supply. In order to facilitate the obtaining of registration in each State / UT, the e-commerce operator may declare the Head Office as its place of business for obtaining registration in that State / UT where it does not have physical presence.
However there is news that some relaxation will be given for registration in every state but till now no notification is issued, so you are required to register in every state. Procedure for registration is given in section 25 of CGST Act and relevant rule 12 of CGST Rules. (Reply dt.16/01/2019)