Shopify has a concept called the "Default Location", unfortunately this does not transfer over to Manage Comics automatically.
You will need to set a Default Location where all QTY will be imported into within Manage Comics.
Within Manage Comics you'll find Default Location in Settings, below your Terms of Service.
Manage Comics will then assign all quantities to this location, and you can do transfers within Shopify to allocate items out to other locations.
Manage Comics only deals with a single location because we believe the proper place to handle quantity changes is within Shopify since we treat Shopify as the "Source of Truth".
To learn more about Store Transfers within Shopify, please visit Create an Inventory Transfer within Shopify.