Unfortunately, none of the Control Panel settings are configurable via C1/eDirectory.
In terms of the portals, you would have to push out some registry settings to specify the name of the portal folder, and the name of the applet to be run when the folder is clicked.
The settings you are interested in are:
Portal Folder Enabled = 1
Portal Folder Name = “The name”
Portal Folder Default = “Binary data”
The value in ‘Portal Folder Default’ is a specially coded binary format. You will nee to manually select an applet via the control panel, then check the registry to obtain the actual data you need to write into the registy.
You can also write these values on install using the /i- switch and a config file. See the installation topic for details.
I hope this helps.