Custom domains are your own domains in format www.example.com, while sub domains are like https://example.myshopmatic.com with the suffix myshopmatic.com present in the URL
Update your primary domain from custom domain to sub domain by going to https://myshopmatic.com/manage/domain_name [Left Menu -> Setup -> Domain] and select the sub domain from the dropdown menu and click on Save.
It is advisable to check the sub domain in a new browser or incognito mode to confirm that the sub domain has been updated correctly.
Do remember that you will need to use this updated sub domain across all mediums. This means adjusting marketing campaigns, social profiles, blogs, posts, etc. to include sub domains wherever custom domains were used previously. All the buyer traffic should be directed to sub domain.