Service Desk customers get an email when they raise a request through the portal, when the request's status changes, when an agent adds a customer-visible comment, and when their issue is resolved.
It sounds like your agents are adding a comment and then transitioning the issue – or vice versa – which, as you point out, sends the customers two emails.
It is generally recommended that agents add comments when they transition the issue. The transition screen will need to have the comment field on it, but by adding the comment during the transition, the customer will get one email.
Another thing to consider is mapping your workflow statuses to request statuses, e.g. mapping "Open" and "In Progress" both to "In Progress." If you do this, then changes between these two statuses will not be made known to the customer.
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