Thanks for checking out the plugin!
There are a couple of ways to set the taxonomy as hierarchical. The most "core" is that you can pass that as one of the array args when setting up the taxonomy, just like you would in register_taxonomy. Since this attribute is so likely to change, I made a special parameter for it in the class construct.
$tax = new Super_Custom_Taxonomy( $name, $singular = false, $plural = false, $acts_like = false, $register = array() )
$acts_like allows you to say this acts like a "tag" or a "category". Since non-hierarchical (tag) is the default, you'd probably only ever pass it "category" unless you wanted to be explicit. Incidentally, you can even abbreviate it to "cat".
So your material construct would become,
$tax_materials = new Super_Custom_Taxonomy( 'material', 'Material', 'Materials', 'category' );
You can find the full documentation on this class here: https://github.com/mboynes/super-cpt/wiki/Super_Custom_Taxonomy-Reference