You don't have to specify/change the sync order if the folders are independent.
Changing the auto sync order is usefull if you have multiple folders with dependencies.
Example:
Mail Folder "Orders" contains formated emails with Order and customer info.
After Saving the order(s) to a database, a VIEW will extract the customer info from email body and presents it as Contact data.
The View is linked to a folder "Customers".
To config GeniusConnect for this scenario, the Mail Folder must be saved to the database, before Loading the customer data.
This will be the config:
Folder->Direction
"Folder Orders"->Store All
"Folder Customers"->Load All