I'm not going to promise this will work because I'm not actually a user of ECLIPSE (I use Ubuntu via text files or Visual Studio on Windows)... but this document describes how to do what your asking with ECLIPSE/Java, so I'd expect its the same with Python!
Hope it works for you, I know how much of a pain IDEs can be when something is unclear!
http://www.nceas.ucsb.edu/scicomp/EclipsePres/CreateEclipseJavaProject.pdf