Copy the collection code in the HTML onto any page on which you wish to display a collection. This example setup only can accomodate one collection per page, but it shouldn't be too hard to mod it for more.
Copy the cart code in the HTML onto any page on which you wish to display the cart.
All scripts should be globally accessed on your site.
A great deal of this was built using the original example code from Shopify itself, found here.