In the eNom control panel if you edit DNS records when not using their name servers you get the following warning :
"The DNS/Zone information on this page will have no effect because your nameservers need to be set to use our nameservers. Our name servers can be set in the 'DNS Server Settings' under 'Manage Domain' drop down."
In the WHMCS eNom module there is no similar warning on the DNS Management page, it would be useful.
The eNom API call GetDomainInfo does flag if eNom name servers are in use. Presumably you are making this API call anyway, so adding the warning should be trivial.