I am implementing a flow on Salesforce where I have enabled email-to-case to register emails coming as case. I will have to notify the customer who is sending the email to our support email that the request is received and would require further information to proceed.
If I have understood your problem correctly then the solution is quite simple. Please go to Setup and in the Quickfind box enter "Case Auto-Response Rule." There you can create an acknowledgement mail for email2case. Rest of the part is pretty simple and I am sure you will be able to figure it out one you explore this path.