The Primary Org is used as the "source of truth" which Mayday HQ aligns all other entities in the group back to. You can change this from any page.
Dashboard
You can change the Primary Org on this page by selecting the star next to the entity you wish to change it to:
Once you select the star the page will reorder putting the new primary at the top of the list.
Chart of Accounts and Tracking categories
You can change the Primary Org on these pages by selecting the star next to the entity you wish to change it to, in the header row:
Doing this will automatically update the page and compare every org to the Chart of Accounts or Tracking Categories in that new Primary Org.