To show in Apparance Preferences > Theme, like Ambiant-MATE and BlueMenta do, the theme has to be a Gnome Metatheme. Otherwise, it only shows under ‘Customize’ for an existing theme.
A Gnome Metatheme consists of a GTK theme, Icon theme, window border theme and pointer. Each Gnome Metatheme has an index.theme file which specifies these things. You can modify the index.theme if you want. You can also make a Gnome Metatheme by adding a correct index.theme to an existing theme folder. Check an existing one to see how it’s made, and/or read:
https://people.gnome.org/~shaunm/admin-guide/themes-17.html
You want themes that have both gtk-2.0 and gtk-3.0 folders included, as our applications might use ether toolkit.