Hello,
I am trying to provide customers with an option to host their sites under our sub-domain.

Everything seems to work perfectly, except for emails.

This is the setup.

I am trying to provide hosting:
customer.domain.com as the main domain for a customer

domain.com itself is already pointing to cpanel DNS servers, for example
ns1.domain.com (using cpanel)
ns2.domain.com (using cpanel)

Now, with WHM I created MAIN ACCOUNT:
customer.domain.com

Everything works perfectly except for email.

domain.com itself currently is not hosted under WHM/Cpanel.

Websites are working perfectly, customers can setup:
sub1.customer.domain.com
sub2.customer.domain.com

But nothing works with email
email@customer.domain.com can not receive any outside emails from Gmail or Yahoo or anything.

I see that everything is setup properly for DNS Zone:
customer.domain.com in ns1.domain.com and ns2.domain.com

Is it possible that I have to add domain.com in WHM/Cpanel too?

Any advice would be greatly appreciated.