After installation, the reboot is from the installed OS on the harddrive - or else it would begin the installation process again...
I don't know the Novell Desktop installation, but if it is anything like SuSE, which is now Novell, then you only need the additional CDs if you decide to install extra packages/applications.
Does the istalled OS work & do everything you want/need it to do?
If so, then you probably do not need to worry about the extra CDs