The reason for all the different upload behaviors is I kept trying different things to get it to work.
I tried it again from scratch. Created the session ID named username on the login page. Then I created a new form uploader.php went through the file upload wizard and added directory path and session variable as above. All the files still go into the main author directory. I even added a username directory into the author directory but no luck. Then I realized I missed the session start on line one of the uploader.php file, added it, uploaded to the site and retried. Still no luck. Should the author/author_files directory be an absolute path, ie., home/author/... or something like that.
I also uploaded the helperphp.php file, are there any other files that should have been uploaded?
Nope, I just tried changing the path to the absolute path and still the same results, the uploaded files go directly into the author directory. Perhaps what I want is not possible?