Can I set the domain quota for emails at the WHM level, to control the data transfer ?

Currently, you can set the amount of emails per hour a domain can send using this Tweak Settings option in WHM: The maximum each domain can send out per hour (0 is unlimited):

How can I flush the Exim queue from the shell?

To flush the queue, execute the following:

• exim -qff

To flush and enable debugging:

• exim -qff -d9