When I respond back to a customer query from my mailbox then the email is not tracked against the case. Similarly when my customer responds back to me directly, the email does not get tracked. Do I need to manually track these emails every time?

Zap Helpdesk App has an excellent feature called as “Forward to link an existing Case”. This allows forwarding the email to support queue and have it automatically tracked against the Case. Best practice would be that even though you are replying from your personal mailbox…ensure that the support email address is marked in the CC section of the email. Similarly if the customer too marks the support email address in either “To” or “CC” section then the email will be automatically tracked against the Case.