You can Manage your queries all at one place from the Contact us Queries section in your dashboard and acknowledge them easily without any confusion.
Here's how you can manage your Customer queries
From the left panel in your dashboard select Online store -> Customers -> Contact Us Queries
You will get access to the details like Name of the customer, Email, Query creation date, and the Query of the customer.
Customers can send you queries through the Contact us section on your Store Website.