I submitted online as I was not in the UK at that time (my visa was close to expiring). I sent the PDF copy to the Printing and Services people with detailed instructions of how many copies required, how many pages, etc.
Then I had to pay for the printing costs via online to the Printing people. Once that was done, they set out to print and bind my thesis, then someone sent my thesis to the Exams office. The whole process took some 2-3 days and many e-mails. Looking back it was such a rush trying to complete everything on time (due to the distance as well) but I had to do it quickly due to visa matters etc.