Create an 'upload' folder in the same directory as the php files. Name it upload and ensure that your web server can write to this folder.
Ensure that you get your MOSS id and put it into the handler.php
When you go to the application, you can select multiple files to "compare" with Moss. If you input a assignment, you will create a folder in the upload folder. If you use the same assignment name for further compares, it will compare the new files and old files that were in that "assignment" folder from past compares. You can delete the older files from the page by pressing the delete button next to each assignement. If you do not input a assignment, it will do the compare ont he two files and then be deleted after you are done.