Hey @kubisovakat
Welcome to the Community Forums!
I can understand how receiving a Shipping Confirmation email right after receiving an Order Confirmation email would be confusing for the customer!
Can you confirm if you are using any third party apps or integrations that are linked to your order fulfilment or shipping process?
When a customer places an order, they will automatically receive an Order Confirmation email. Usually the Shipping Confirmation email would then get sent when the order has been fulfilled (if you select this notification).
What I think might be happening here is that orders are getting automatically fulfilled after the customer places them, which is causing the Shipping Confirmation emails to get sent automatically. You can check this in the Settings > Checkout section of your admin. Head to the Order Processing section and check to see which option is selected.
Automatically Fulfil Orders would generally only be used if you are selling digital downloads or if you’re using a fulfilment service (this is why I asked earlier if you are using any third party integrations). Since you need time to prepare and ship the order, then perhaps Manually Fulfil Orders would be a more suitable option? If you wish to use the Automatic setting, then you should see an option there which says Notify customers of their shipment via email - deselect this to turn off the automatic Shipping Confirmation emails.
We have some helpful information here which explains this in more detail.