Create a folder with a short title of the presentation. You'll use this in the URL.
Create your presentation using Markdown and save it in a file named "slides". You can use the demo presenation and Daring Fireball's Syntax page http://daringfireball.net/projects/markdown/syntax to see what you can do.
Use three asterisks (* * *) to start a new slide.
Add metadata to the top of the file. See the demo slides for example.
Navigate to the web directory where PHPdeck is installed and append "?d={FolderName}" to view your presentation.