Hi Mohan,
You can create a Theme under your internet service as:
Right-click on Service -> Create -> theme.
This will create a folder under your internet service by name 'Topic <themename>'.
Right-click on that -> Create -> MIME -> Select a folder or files that define your theme (with CSS, JS, JPG files).
After the folder is uploaded, you can define the theme for your generated HTML templates present under this internet service as:
~theme = <yourthemename>
You might also need to add a link to your main CSS file in your template section: ~itsmobileCssInclude, so that it recognizes it.
Also, since this is your custom theme, you will need to ensure the CSS class names, logo names, etc match with that of the standards that are there in the auto-generated HTML templates.