Sorry, if the tool seems daunting but it really isn't. It's quite easy when you get down to it and I think I've included enough examples as to how people work [-i.e. multiple directories, multi-dirs. + library directory, single directory with files, batch files, makefiles, etc., etc.] and I've even given you an example of how I develop (my directory structure for C++ projects) and made a working lisp example project.
...basically the principle is single working file that CAN BE used to create multiple outputs (final products) if needed.