Setting up a marketplace in the deep web, is simply the same thing as setting up a market in the regular net, but all you need to do is to set up a CentOS 6 / Linux server,and install few programs such as "yum" on the server.

Those programs make sure that only through a deep web browser you will be able to grab data from your website.

I think this guide may help you with that:

https://www.deepdotweb.com/2015/03/27/onionshop-guide-how-to-set-up-a-hidden-service/

Also keep in your mind that people won't be able to find your site, you will need to advertise it on the deep web somehow, also keep in your mind that you won't be able to choose the domain for your site by your own.

I hope I could help you, don't hesitate to use google!