Shipping is calculated after the checkout form is submitted, I just tested your cart and after filling in the checkout form to set the shipping location, can see the shipping applied. see attached screen shot.
you cannot edit the checkout wizard, but you can edit the server behaviors that it applies to the pages.
For the checkout wizard, you can use the theme option to change the colors to be closer to the Yosemite preset.
in the WA_eCart/CSS/eC_Clean_Yosemite_Arial.css file, edit the width for the .eC_Clean_Yosemite_Arial table and .eC_Clean_Yosemite_Arial selectors.
the add to cart behavior is not edited from the bindings panel, you need to edit the add to cart behavior from the server behaviors panel.