When using the WHM interface, there is a global option to enable SPF & DKIM records to all domains on the server. This interface inside WHM is the following:
WHM: Home -> DNS Functions -> Enable DKIM/SPF Globally
However, using the cPanel API calls, you can enable or disable the DKIM record on individual domains. There is no way to do this through the WHM interface.
To enable or disable a DKIM record for a domain, you will want to reference the following WHM API documentation:
Both of these API calls have a "command-line" component. Below are examples you can use.
To enable DKIM:
whmapi1 enable_dkim domain=cptest-2.com
To disable DKIM:
whmapi1 disable_dkim domain=cptest-2.com