New VPS and need to setup PHP mail per domain

I bought a VPS so I could manage many clients at once and have an issue with wordpress notifications going into spam folder.

It turns out wordpress will use the root domain for the vps instead of the domain the account is associated with in cpanel. Because of this emails from wordpress notifications are being sent with an account address instead of the address.

Is there a way in WHM or cpanel where I can force it to use the domain?