I should start with the disclaimer that I am running Snow Leopard on my Mac.
I use various scientific packages [numpy, matplotlib, scipy, sympy]. In the past, I have found I was not able to install some or all of these packages using the Install feature of PyCharm's Project Interpreter Preferences. When such problems occurred, it was a no-go whether PyCharm's PI was a virtual env or not. A workaround I discovered was, since I use a Mac and since I have Mac Ports installed, to install the Mac Ports version of whatever package I wanted to a virtual env created not by using PyCharm's Project Interpreter Preferences but by using the Mac Ports port of virtualenv instead.
My experience is that Mac Ports packages are more compatible with my Mac than the ones that PIP [which PyCharm uses I think] pulls down. It is not that big a deal to create venvs with virtualenv from a term session, and install packages with Mac Ports instead of PyCharms' Install feature, so I can live with the Way things are.
Nevertheless, since Python v3.3 now has a built-in alternative to virtualenv which PyCharm's Project Interpreter uses, I decided to revisit the problem. Alas, not only has nothing changed, but even if I create a venv using python v3.3's pyenv from a term session, and then install Mac Ports numpy and sympy packages, PyCharm still does not see those packages. PyCharm will only see those packages if the venv was created using Mac Ports' py33-virtualenv port.
And, yes, I do use the –system-site-packages switch when creating venvs from a term session.