I know this late, but I thought it would be nice to clarify the situation: PyCharm and Conda and pip work well together.
Short answer
Just control Conda from the command line . PyCharm will automatically notice changes as soon as they happen, as with pip .
Long answer
Create a new Conda environment:
conda create --name foo pandas bokeh
This environment lives under conda_root/envs/foo . Your python interpreter is conda_root/envs/foo/bin/pythonX.X and all of your site packages are in conda_root/envs/foo/lib/pythonX.X/site-packages . This is the same directory structure as in a virtual virtual network. PyCharm does not see the difference.
Now, to activate the new environment from PyCharm, go to file> settings> project> interpreter, select Add locally to the project interpreter field (small gear) and track your python interpreter. Congratulations! Now you have a Conda environment with pandas and bokeh!
Now install some more packages:
conda install scikit-learn
OK ... return to your interpreter in the settings. Magically, PyCharm now sees scikit-learn!
And the opposite is also true , i.e. when you install another package in PyCharm, Conda will automatically notice. Say you set the queries. Now list the Conda packages in your current environment:
conda list
The list now includes queries, and Conda correctly determined (third column) that it was installed using pip.
Conclusion
This is certainly good news for people like me who are trying to get away from pip / virtualenv installation problems when packages are not pure python.
NB: I am running PyCharm pro edition 4.5.3 for Linux. For Windows users, replace the command line in the GUI (and the backslash with a backslash). There are no reasons why it should not work for you.
EDIT: PyCharm5 does not work with Conda support! In the community too.