When sending orders with Yamato through Shiptheory, your orders will be added to a manifest throughout the day. As you book in orders, they'll sit in Shiptheory waiting to be manifested. This will continue until your specified "Manifest Cut-Off Time", at which time, the manifest will send to Yamato. Orders put through after that time will then be added onto the next day's manifest.
You can specify your Manifest Cut-off time in your Yamato settings page in Shiptheory here:
If you want to see the orders that are currently waiting to be manifested in your account, you can do so by clicking "Yamato Europe" in your Shiptheory account dropdown, then clicking "Manifest":
On this page, you can see the shipments waiting to be sent through:
In terms of how the manifest occurs, Shiptheory will automatically email Yamato a CSV file of all the shipments on that day's manifest. This won't require any manual intervention from you, it will happen daily to ensure all your orders are sent through to the Yamato Europe system as needed.
However, if you have any issues with this, please Contact Support, who can then take a further look into this.