Is it working properly now? Last time I've tried it I had to go back to oh-my-zsh because prezto screwed my terminal.
By the way, one of these days debugging the slow startup time of oh-my-zsh I found the culprit, virtualenvwrapper. Again I didn't have the time to good deep into that, so I just edited out that line from my .zshrc.
Seems to be using properly for me. I've been using it for a month now and I didn't have any issues with it. But that may be because I'm only using the basic plugins which are enabled by default, nothing fancy.
[1] - https://github.com/sorin-ionescu/prezto