Both Power Store and Cafe Commerce are pre built web sites.
In other words, the web pages are already created with functionality for an admin back end where you can enter product information, a regular user front end to show the product catalog and add items to the cart and checkout.
With Power Store, you need to install the package to your web server to begin using it. Cafe Commerce is a hosted solution though, so there is no install, just sign up and start adding product information.
Where cafe commerce is a hosted solution, there is no access to the source code for making modifications. with Power Store, you have more flexibility in being able to edit the pages source code.
The smoothest process would probably be Cafe Commerce.