Only the overlay-style cart that appears "inside" your own page can be customized. Note that customization of the overlay cart is page-specific, so make sure you add cart customization code to your View Cart code on every page where you want customizations to appear.
Whenever the overlay cart cannot work for any reason -- e.g., due to missing or garbled View Cart code in the affected page, or disabled javascript in the buyer's browser -- the buttons work in "fallback" mode by opening a separate window/tab to display the cart. Aside from a custom logo/header you can upload in Seller Admin > Edit Preferences, this version of the cart cannot be customized. We also use this fallback cart on mobile devices to make best use of the limited screen area and allow buyers to use their touchscreen pinch/swipe gestures to zoom and pan the cart.
Also note that items a buyer adds to the overlay cart will not appear in the fallback cart and vice-versa, so make sure the cart buttons on all pages of your site are showing the same type of cart display. Usually this is just a matter of making sure every page has at least one block of your View Cart code.