According to the facts I learned from the internet, the process is very simple. You just have to precisely follow the steps given and all will be done.
Now you will have the following things in hand before visiting the University: Set of Original Documents, 2 Sets of photocopies, Application form, Challan, WES Reference Number. But this is incomplete, as you will need to fill WES form.
WES Form:
Visit after 8 days. Show the challan student copy. Check the documents for Sign and Stamp on all photocopies - including the WES form. Put all the documents inside including the WES form in the envelope, for being stamped.