To modify virtual hosts configuration on account level basis, we can use includes as documented by WHM under the generated httpd.conf
First, ssh as root and do:
sudo nano /etc/httpd/conf/httpd.conf
Locate the virtual host for the account (ctrl + w to search) and find the comment for the location to create the includes.
Create the directory for the given location
mkdir -p <location>
Create the .conf file to be included