You can manage MX entry in for all your hosted domains in WHM. For this you have to follow below steps.
- Login to WHM.
- Click on "Edit MX entry" option under "DNS Functions".
- Here choose particular domain and click in "Edit".
- You can edit your domain's MX records now and after that click on Save. If you want to use email services of other email provider then you can easily change MX record with this tutorial.