At the time of registration will the assessee have to declare all his places of business

Yes. The principal place of business and place of business have been separately defined under section 2(85) & 2(89) of the CGST Act respectively. The taxpayer will have to declare the principal place of business as well as the details of additional places of business in the registration form.

(ICAI FAQ PUBLICATIONS 06-09-2017 REGISTRATION: FAQ NO. 36)