I had a similar problem running SciPy on my computer. There are two ways to fix this problem: 1. Yes you do need to cd into your python directory. 2. Sometimes you have to tell the computer explicitly what path to go through, you have to find the program you're using, open up the properties, and reroute the path it takes to run. 3. consult the manual: http://matplotlib.org/users/installing.html or http://www.scipy.org/install.html
the Scipy package is very finicky, and needs things spelled out in obnoxious detail.