Next time; never order chained-root (intermediate) certificated. Use single root instead. It give's you less headake. If you've root access, you can try to manually edit the users httpd.conf. If not; first install the intermediate certificate, then the domaincert.
Randy, all of your points are red herrings. chain-root Certificates are actually more secure than single-root certificates (in fact the most expensive Certificates from Verisign are chain-root Certificates. And DirectAdmin has fully supported chain-root Certificates for years.
You do not have to touch httpd.conf, and you most likely shouldn't, since it may be overwritten.
The right way to install the Certificate is to open up any file ending in .crt in a text editor (Windows desktop will usually try to open it as a cert, so either open Wordpad first, and then use it to open the .crt file, or use
open as.
Install it under the key, as defined in DirectAdmin documentation.
The right way to open the chain-root bundle (you've called it the Intermediate Certificate) depends on what kind of a file it is. If it's a .crt or .txt file, open it as above, with Notepad. If it's a zipfile, open it with WinZip or similar, then with Notepad.
Then follow DirectAdmin documentation (see site-helper.com).
The most important (yet undocumented) step is to wait a minute before testing, as it can take up to a minute for DirectAdmin to properly set up the files and restart httpd.
Jeff