In Paypal, there are instructions on how to do this on your website whether you're using a shopping cart or not.
I have a website and it uses a free shopping cart and Paypal is one of the forms of payment. The shopping cart is actually designed to take Paypal. I'm assuming you want it automated so you don't have to send invoices.
Take a look at the Paypal site and if you're in the market for a free shopping cart, google "Mal's ecommerce" and you'll find a very nice shopping cart.