It's possible to edit the templates, but not recommended. First, it would require that you know/understand the current templating system as well as how the web server interfaces to the Indigo Server (which isn't really published). Second, it will break every time you update Indigo. Third, Indigo Touch doesn't render using HTML, so it would only apply to the web pages. Fourth, the next major release of Indigo will have a completely rewritten web server, with completely new underlying technologies, so anything you did in this respect now wouldn't be applicable.
You can
add your own images however, so you can probably get you partially the way there.
Alternately, you can use the
REST API to build your own web pages.