I may have miss understood what you said here so bear with me. Booting
from the USB may be your biggest problem. The image on the USB is
handled in a different way than when a Linux distro is installed.
Intentionally you are not allowed to distroy files on the HD by
overwriting so the installed OS can't use the hard drive. I have not
likely presented this information to you to make it easy to understand.
What is important is it is likely a permission thing. When You start the
OS from a live CD you are told that your work won't be saved.

I wonder how many times you have tried using other OSes like Windows
from a live CD or USB. Other than specific tasks you would or are
limited to what you can do with such disks like resetting a password.
The file system is really quite simple when you take the time to view
the logic. I would suggest dedicating some of your HD to install linux
before you claim Linux falls short in the filing system area.

My external USB drive has any movies I am working on on it. I drag and
drop what I will be working on onto the desktop to speed up disk access
to the file. When through, I copy the file onto the external and it is
updated by over writing with the newer file, or re-named with "save as"
much the same way I used windows before I knew better and migrated to
Ubuntu.