A site collection administrator in SharePoint Online has full admin rights to a SharePoint site no matter what rights are set within the site. They do not show within the permissions for that site. If you need full control of a site collection this is an excellent way to achieve this.
For an M or E plan
From the menu bar, in the top right select Admin, the SharePoint from the drop down menu that appears.
This will take you to the SharePoint admin centre as shown above.
Select the site collection you wish to assign a new site collection administrator as shown above.
Then from the buttons at the top select Owners. From the menu that appears select Manage Administrators.
Now add the new user into the Site Collection Administrators box in the lower part of the screen.
You can also replace the Primary Site Collection User if you want but remember there can only be one of those.
Once you have added the new user press OK to save the changes and any new Site Collection Administrator will have full rights to every site and subsite with that Site Collection independent of what rights are set actually inside the site.
Finally, remember that this only assigns rights to the Site Collection you selected. You will need to repeat this process for other Site Collections you have if you also need to assign rights there.
