I don't have PyCharm on this machine, but have used it with Blender on my dev machine. So I can't detail the setup now - but for starters, see this dev doc regarding debugging Blender with Eclipse: https://wiki.blender.org/index.php/Dev:Doc/Tools/Debugging/Python_Eclipse
should be close enough for you to use with PyCharm (which is a custom eclipse). I presume you're okay with local (single machine) debugging - that's what I have setup in Eclipse/PyDev, tho in other Python work, I came across a browser-based setup that I adapted to PyDev - so now I debug Blender in the Browser - with the api docs in the 'tab next door' - very convenient.
if you're interested in remote debugging instead, see this recent dev blog entry: http://code.blender.org/2015/10/debugging-python-code-with-pycharm/
m23d