How to add custom conf to some WHM account

You have to first create a directory corresponding to the path above. You can do this as follows

mkdir -p /usr/local/apache/conf/userdata/std/2/username/
cd /usr/local/apache/conf/userdata/std/2/username/
vi virtualhost.conf

Remember to change to the domain for which you are going to create the custom virtualhost configuration and username to the cpanel username of the user corresponding to the domain.

Once you are done with making the modification you can re-create the httpd conf file by running the following command

/scripts/ensure_vhost_includes --all-users