I'm using the new Pycharm 1.0 (congrats on the release!) and it looks like this issue has been fixed http://youtrack.jetbrains.net/issue/PY-1990 , however it doesn't seem to be loading my customized manage.py specified in my project under the project_root/bin folder so I'm still unable to use all the built in tasks for django. I have the working directory in the server configuration set to ~/cobastella/bin so I was hoping that Pycharm would look in there for my manage.py first before using another copy.
If I go ahead and create my own python task and specify the manage.py file it works fine and uses the customized file with the added site.addsitedir settings. While this works I can't take advantage of all the built in Django goodness.