What happens if I replace Shopify email app with a third-party app?

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Hi guys!

I have a question, what happens if I delete the shopify email app and use a third-party app when I have an order? Does shopify email app send an additional "thank you" email? And if I enter the tracking number manually, will the shopify email app automatically send tracking emails to customers?
Currently, which tracking number app can I use to integrate with omnisend? I want to set up my workflow on omnisend (order confirmation, estimate tracking time, shipping status, tracking number, etc...) 

Glad to receive answers from you, guys! 

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