We do not automatically replace the automation flows in your Shopify store. Therefore if you create an email notification for order created, your customers may receive 2 emails at the same time (1 from Shopify & 1 from ManySales).
The best practice is to use ManySales Automation Flow to send a follow-up message on top of the Shopify one, like an upsell campaign, or a simple thank you note.
However, since Shopify does not support SMS notification at the moment, you can still use ManySales Automation Flow for updating order status via SMS message.
If you have any further concerns, please feel free to contact us via live chat or email us at email@example.com