I'm not sure what you mean by a server wide Certificate. A Certificate can only be used for a specific domain, or visitors will get an error message (and on the newest browsers the error message will scare them out of visiting the site).
Do you mean you want a shared certificate that all your users can use? If so, then there are several options you can use:
1) You can use subdomains. For example, if your client's domain is joesdomain.com, and your main domain is example.com, you can create a subdomain of your main domain: joesdomain.com.example.com (you actually type joesdomain.com into the subdomain field). To do this you'll need to have example.com on it's own IP#, you'll need to buy and install a commercial wildcard Certificate for example.com, and you'll need to create separate ftp accounts for each subdomain, with access to that subdomain only, to give to your clients.
2) You can create a domain, for example secure.example.com and do the same as above.
3) You can create a domain as directly above, and instead of using subdomains use subdirectories. You'll still need to create the ftp logins.
The third way you can use a much less expensive Certificate; you won't need a Wildcard Certificate.
No matter which way you use, your client's will have to link to their secure content with the correct subdomain or subdirectory.
And you won't be automaticallly charging the client for either space or transit used, unless you develop your own method of tracking and charging.
These limitations are NOT of DirectAdmin, but rather of the way Certificates work.
Jeff