To start off, simply place your config.json file and your errorTemp.jpt file (download starter files above) into the same directory as your binary/JavaScript source, if you are using the JavaScript source, make sure the mimes.dat file is also there. If you have any files missing, you can get them from the JOTPOT Server github repository linked in the top right of the page. Then make sure there is a directory names "sites" in the same location, with subdirectories of the hosts you would like you server to host (remember about host aliases in your config.json file).
When all of that is done, you should be able to run your server, if you have a binary, just run it within the same directory, or if you have the JavaScript source, run that with the recommended version of Node.js (1.6.4) within the same directory.
Any file that's name ends in ".jpe.js" within this directory will be loaded as an extension - see the docs for more info on extensions or the config.json file.