I'm confused

Depending on the context involved there may be a different meaning or description for what may define a specific type of script, plug-in, module, or add-on. From the description provided I believe the item being referred to would be that of a cPanel plug-in. As a cPanel plug-in it would be accessed and executed by the user that is logged-in via cPanel (not that of "root"). There may be other components involved that are not accessible by a regular end-user such as a WHM plug-in or crontab entries for maintenance tasks as found in a number of third-party plug-ins and add-ons.

For developer reference information I recommend the following resource: cPanel Developer Center

 

To clarify my understanding, are you wanting to develop software like Fantastico, or just install existing software that is already developed by a third-party?

To confirm, do you have root (Server Administrator) access to the system, such as via SSH and WHM access (where the username is "root")?

 

I would consider using the Install File Generator for the custom cPanel Plugin via the following resource: cPanel Plugins - Developer

Using the the Install File Generator for the cPanel Plugin one can define an access URL for the custom software; this is normally relative to the theme directory (e.g,. relative to "/usr/local/cpanel/base/frontend/<theme_name>/"). The access URL might involve a path that uses a symlink to point back to the installation directory for the custom software (e.g., such as a new custom directory within "/usr/local/cpanel/3rdparty/").

As an example, here is what I see used by Fantastico, that of using a symlink within the theme directory that points back to the install path:

Code:

# stat /usr/local/cpanel/base/frontend/x3/fantastico | head -n1
  File: `/usr/local/cpanel/base/frontend/x3/fantastico' -> `/usr/local/cpanel/3rdparty/fantastico'

Another example, as seen by a different third-party product, also makes use of a symlink pointing back to the install directory, but here the symlink is in a different path that is still accessible while logged-into cPanel, as seen below:

Code:

# stat /usr/local/cpanel/base/3rdparty/example | head -n1
  File: `/usr/local/cpanel/base/3rdparty/example' -> `/usr/local/cpanel/3rdparty/example'

The custom software installer that you would develop should handle the process of registering the cPanel Plugin and also rebuilding icon sprites as detailed in the documentation; for more verbose details and information regarding the install process of a cPanel Plugin please refer to the following documentation: cPanel Plugins Installation Instructions