You don't set PYTHONPATH, you add entries to sys.path. It's a list of directories that should be searched for Python packages, so you can just append your directories to that list.
sys.path.append('/path/to/whatever')In fact, sys.path is initialized by splitting the value of PYTHONPATH on the path separator character (: on Linux-like systems, ; on Windows).
You can also add directories using site.addsitedir, and that method will also take into account .pth files existing within the directories you pass. (That would not be the case with directories you specify in PYTHONPATH.)
