Cant get a game to copy properly

[Strike]

i have a sony rewriter and have downloaded clone cd and database, database reports that protect cd is in use on Champ Manager99/00 and that there are some dummy files, when i then tried to copy the disc i am told there is insufficient room on the disc, i am using a 650mb traxdata disc and can only presume that i am trying to copy the dummy files as well. can somebody please explain the full process of how to make a complete backup copy of a game?
Thanks