A theme is identified by it's unique alias. If you have your theme under the
app/View/Themed/MyTheme, then your theme's alias is MyTheme.
A theme.json file is also required. You can see the JSON file used for the default theme here: theme.json.
For example, you have a theme with alias MyTheme. All your files should be placed like this:
Do not forget the theme.json file. Your theme will not be available in the admin panel otherwise.
If using a version of Croogo 1.4 from before Dec 24th 2011 then your theme requires a theme.yaml file as explained here: 1.3 > Designers > Themes > Yaml file.