With the invitation Code given to you in the email, you need to create an account by going to
https://portal-portail.apps.cic.gc.ca/signup?lang=en
Once your ceremony is done, you email back the oath forms, not more than 1MB, (signed in front of the clerk) to the same email address that they have sent you. The subject of the email should be according to the instructions of the pdf and your clerk will let you know their initials to add in the subject line. You can use 1 email to send more than 1 oath form but minors below 14 don't require their oath forms to be signed and emailed back to them.
Then you wait 2-5 business days and log on to the IRCC portal you created to download the certificate. Try every half hour during business hours so you don't get locked out of your account for 24 hours.
Doesn't matter if you applied by paper or online, you will have to follow the steps above in any case.