You set up the cart (open source or paid for) and the interaction of the cart with the gateway or Paypal, but it is Paypal or the gateway that do the actual money transaction. Depending on the cart you are using, the set up can be really easy or more complicated.
If you have to advise the client on which payment platform or type of cart to use, you will have to do some homework, as there are often hidden costs, setup fees etc. I'm sure Eddie (Newseed) will chip in with a lot more information.
Make sure your client pays you for the time you are going to be spending on this project.