If they have pointed theirdomain.com and ftp on theirdomain.com to a specific IP on your server, it does not matter what nameservers you use as long as the only account hosted on "216.XXX.XXX.100" is their account. If it's not, you should put their account on a dedicated IP on your server and give them this IP instead. If multiple websites are hosted on the same IP, you cannot point the domain to this IP as it will not show any of the websites (it will show the default "cPanel has been successfully installed and your apache is working!" page). If you cannot do this (i.e. you don't have the IPs to do this), then you must provide them with your nameservers and tell them that they have to change their nameservers to your nameservers in order to use your services.
I hope that's clear, you might have to read that slowly as it's a little confusing!
█ Guy Riese - Tech-Hosts Ltd. - Registered company in England & Wales (Based in UK - Europe)
█ High quality & affordable Web Hosting, Reseller Hosting, Master Reseller Hosting, Linux VPS & Dedicated Servers
█ Lowest priced domain names in the industry - instant registration and management
As long as the domain is using their NS and they have pointed the A records correctly to your servers in the zone file, you need to create the hosting account on your WHM with IP 216.XXX.XXX.100. The domain should work fine. The domain resolving will be taking place from their server and you don't need to worry about that part. There is no difference if you use your or their NS while you create the hosting account on your server.
While creating an account in cPanel you can select that you want to use their nameservers; it is important to choose this option especially if they decide to host mail on another server (mx records) if you do not take care of this properly you may get in trouble later when one of their scripts is going to send mails out to their own domain; or if any other person on your server mails to the domain.
This happens because in a default setup the mail will still be delivered locally. And remote mx records are not observed.
So it is important to make sure you set this up correctly; although the chance a customer runs into this issue is slim; it may cause great confusion with your support department and the customer if it happens.
The option is one of the last check boxes when creating an account:
Use the nameservers specified at the Domain's Registrar (ignore locally specified nameservers)