Registering a new theme is fairly simple. To start you copy one of the existing themes and rename it to your new theme name.

After that you can load it up in your loader file by using the following code:

$reactor->site->themes["jellyfish"] = array("name" => "Jellyfish",
                                      "author" => "Patriek Jeuriens",
                                      "file" => "theme/" . SITE_THEME . "/styles/colors/jellyfish.variables.css",
                                      "description" => "Transparent theme with blue accents.");

Now the theme can be selected by the administrator in the configuration screen. If you want switch your new theme to the default you can set:

$reactor->defaults->theme = "slate";