I'm attempting to get Eclipse + PyDev set up so I don't need to alter the PYTHONPATH from within Eclipse, but rather it will inherit the PYTHONPATH from the .profile document from inside my home directory. Is that possible, or do I need to actually add the PYTHONPATH locations using Eclipse's PYTHONPATH editor? I ask because I am getting different errors when going from Terminal-based python to python in Eclipse, using the same files.
You need to configure it inside Eclipse. Now, provided have a shell that has the PYTHONPATH properly setup, you should be able to start Eclipse from it and when adding an interpreter (you may want to remove your currently configured interpreter), it should automatically pick all of the PYTHONPATH you had setup from the shell (some of those may be unchecked in the wizard at that time, so, you have to go on and check those too -- just don't add the paths from files you'll be editing inside your project, as those should be added to the PYTHONPATH for your project so that PyDev is able to track changes on those files to properly offer you code-completion).
How to make Eclipse inherit $PYTHONPATH on Mac OS X