Hi,
You cannot create one theme under another. So the automatically created theme 99 under your "custom" internet service (not webgui), is the theme that you will use.
Under that you create your MIME object, under which will be your CSS, JS and image files.
The generated HTML templates of your screen present under THE SAME internet service will point to theme 99 by default:
~theme = 99.
You will just have to point to your CSS file under the MIME object.
For detailed steps, refer my blog: ITS templates – Styles, Themes and Legibility (MIME Repository)
At first you said changing the theming of webgui service, so i thought it was something else.