If you want to use the Jekyll PaperWiki theme I recommend downloading this site and serving it locally, rather than creating your own site and installing it yourself - there are a couple of finicky config options that may prevent your site from building. With this preconfigured site, all you have to do is start writing articles. The site is self-documenting, so read the about page for information on how the site itself is structured, and the sample wiki page for how writing entries works. The files comprising the site also contain notes on their usage.
Download, navigate into the directory, and run
$ bundle exec jekyll serve
Navigate to your localhost and start poking around, or see my guide for more details.